Hi
I am getting a series of error messages while performing TBSS
pre-processing. The commands that I have used are
tbss_3_postreg -S
tbss_4_prestats 0.2
I have copied the error messages below
Please can anyone help me understand what I am doing wrong? Thank you
very much for your help
best wishes,
Prerona
===========================================================
Error 1
===========================================================
Image Exception : #22 :: ERROR: Could not open image 19377_fa_FA_to_target_warp
An error occured while reading file: 19377_fa_FA_to_target_warp
19725_fa_FA
Image Exception : #22 :: ERROR: Could not open image 19725_fa_FA_to_target_warp
An error occured while reading file: 19725_fa_FA_to_target_warp
21413_fa_FA
===========================================================
===========================================================
Error 2
===========================================================
merging all upsampled FA images into single 4D image
/usr/local/fsl//bin/tbss_3_postreg: line 178: 23362 Killed
${FSLDIR}/bin/fslmerge -t ../stats/all_FA `$FSLDIR/bin/imglob
*_FA_to_target.*`
creating valid mask and mean FA
Cannot open volume all_FA for reading!
Cannot open volume all_FA for reading!
Cannot open volume all_FA for reading!
skeletonising mean FA
Image Exception : #22 :: ERROR: Could not open image mean_FA
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl//bin/tbss_3_postreg: line 196: 23373 Aborted
$FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
now view mean_FA_skeleton to check whether the default threshold of
0.2 needs changing, when running:
tbss_4_prestats <threshold>
creating skeleton mask using threshold 0.2
Cannot open volume mean_FA_skeleton for reading!
creating skeleton distancemap (for use in projection search)
Cannot open volume mean_FA_mask for reading!
Image Exception : #22 :: ERROR: Could not open image mean_FA_skeleton_mask_dst
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl//bin/tbss_4_prestats: line 96: 23381 Aborted
${FSLDIR}/bin/distancemap -i mean_FA_skeleton_mask_dst -o
mean_FA_skeleton_mask_dst
projecting all FA data onto skeleton
Image Exception : #22 :: ERROR: Could not open image mean_FA
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl//bin/tbss_4_prestats: line 99: 23382 Aborted
${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh
mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm
all_FA all_FA_skeletonised
now run stats - for example:
randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d
design.mat -t design.con -n 500 --T2 -V
(after generating design.mat and design.con)
On 5 June 2013 19:00, FSL automatic digest system
<[log in to unmask]> wrote:
> There are 53 messages totaling 8062 lines in this issue.
>
> Topics of the day:
>
> 1. Problems with Probtrackx step length (2)
> 2. segfault from betting (6)
> 3. mask format for setup_masks?
> 4. Determining individual significance, if any, after group Melodic analysis
> 5. age as a regressor and age-group interaction term
> 6. Dual Regression, Image Exception : #22 :: ERROR, filenames can be
> basenames or not - RSVP (2)
> 7. use of -usesqform
> 8. Nonlinear registration of atrophied brains (3)
> 9. FLIRT problem (5)
> 10. Number of no diffusion images for DTI and TBSS analyses
> 11. I can not install FSL on mac 10.5.8 Quad-Core Intel Xeon
> 12. topup function (5)
> 13. TBSS reregistration (2)
> 14. Message from JISCMail Helpline: lists with public archives
> 15. sienax with betted image... (2)
> 16. design.mat & design.com in randomise (2)
> 17. cluster command question (2)
> 18. beta series correlation (2)
> 19. FDT registration
> 20. Neonatal TBSS (4)
> 21. Resting state fMRI using MELODIC (2)
> 22. length of ISI?
> 23. Registration quality
> 24. fslmeants error
> 25. visualizing results
> 26. 2X2 ANOVA interaction
> 27. MELODIC output report, Powerspectrum scaling
>
> ----------------------------------------------------------------------
>
> Date: Tue, 4 Jun 2013 17:55:08 -0700
> From: "Thomas H." <[log in to unmask]>
> Subject: Problems with Probtrackx step length
>
> Dear FSL experts,
>
> I'm currently working with a set of high-resolution (spatial and angular)
> diffusion images from paraformaldehyde-fixed post-mortem brains. I learned,
> from past discussions on this list about Probtrackx, that the recommended
> step length for fiber tracking is 1/4 of the voxel size. However,
> tractography runs using this step length and a very large number of steps
> (I've tried up to 500000), compared with those computed using the voxel
> size as the step length, yield very poor results: while the larger step
> length (= voxel size) gives nice, long tracts that enter subcortical
> structures and the brainstem in a way that makes anatomical sense, the
> smaller step length (= 1/4 * voxel size) only produces rather short tracts
> are significantly less extensive. Increasing the number of steps and/or the
> maximum number of steps do not improve the results, as I used pretty big
> values for both parameters to begin with. At this point, I'm very tempted
> to go ahead and use the larger step length.
>
> So my question is, are there any parameters I can change to improve my
> results at the step length of 1/4*voxel size? If not, what is the maximum
> step length I could use without significantly sacrificing the accuracy of
> my tracts?
>
> Thanks in advance.
>
> -Thomas
>
> ------------------------------
>
> Date: Tue, 4 Jun 2013 20:23:32 -0500
> From: Matt Glasser <[log in to unmask]>
> Subject: Re: Problems with Probtrackx step length
>
> What kind of resolution for what kind of brain are we talking about here?
>
> Peace,
>
> Matt.
>
> From: "Thomas H." <[log in to unmask]>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Tuesday, June 4, 2013 7:55 PM
> To: <[log in to unmask]>
> Subject: [FSL] Problems with Probtrackx step length
>
> Dear FSL experts,
>
> I'm currently working with a set of high-resolution (spatial and angular)
> diffusion images from paraformaldehyde-fixed post-mortem brains. I learned,
> from past discussions on this list about Probtrackx, that the recommended
> step length for fiber tracking is 1/4 of the voxel size. However,
> tractography runs using this step length and a very large number of steps
> (I've tried up to 500000), compared with those computed using the voxel size
> as the step length, yield very poor results: while the larger step length (=
> voxel size) gives nice, long tracts that enter subcortical structures and
> the brainstem in a way that makes anatomical sense, the smaller step length
> (= 1/4 * voxel size) only produces rather short tracts are significantly
> less extensive. Increasing the number of steps and/or the maximum number of
> steps do not improve the results, as I used pretty big values for both
> parameters to begin with. At this point, I'm very tempted to go ahead and
> use the larger step length.
>
> So my question is, are there any parameters I can change to improve my
> results at the step length of 1/4*voxel size? If not, what is the maximum
> step length I could use without significantly sacrificing the accuracy of my
> tracts?
>
> Thanks in advance.
>
> -Thomas
>
>
> ------------------------------
>
> Date: Tue, 4 Jun 2013 21:40:27 -0400
> From: Satrajit Ghosh <[log in to unmask]>
> Subject: segfault from betting
>
> hi all,
>
> i'm running into a segfault trying to bet this file. any thoughts?
>
> https://dl.dropboxusercontent.com/u/363467/mean_cannot_bet.nii.gz
>
> cheers,
>
> satra
>
> ------------------------------
>
> Date: Tue, 4 Jun 2013 22:11:44 -0400
> From: Satrajit Ghosh <[log in to unmask]>
> Subject: Re: segfault from betting
>
> found the issue - the file had nans in it. perhaps that could be tested
> during read.
>
> cheers,
>
> satra
>
> On Tue, Jun 4, 2013 at 9:40 PM, Satrajit Ghosh <[log in to unmask]> wrote:
>
>> hi all,
>>
>> i'm running into a segfault trying to bet this file. any thoughts?
>>
>> https://dl.dropboxusercontent.com/u/363467/mean_cannot_bet.nii.gz
>>
>> cheers,
>>
>> satra
>>
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 04:35:42 +0100
> From: Stephen Smith <[log in to unmask]>
> Subject: Re: segfault from betting
>
> Hi - FSL has never allowed NaNs - they can be removed using fslmaths.
> Cheers.
>
>
>
> On 5 Jun 2013, at 03:11, Satrajit Ghosh <[log in to unmask]> wrote:
>
>> found the issue - the file had nans in it. perhaps that could be tested during read.
>>
>> cheers,
>>
>> satra
>>
>> On Tue, Jun 4, 2013 at 9:40 PM, Satrajit Ghosh <[log in to unmask]> wrote:
>> hi all,
>>
>> i'm running into a segfault trying to bet this file. any thoughts?
>>
>> https://dl.dropboxusercontent.com/u/363467/mean_cannot_bet.nii.gz
>>
>> cheers,
>>
>> satra
>>
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 05:28:55 +0100
> From: Stephen Smith <[log in to unmask]>
> Subject: Re: mask format for setup_masks?
>
> Hi - I am guessing from the randomise page that 1=exclude - but you could just try it!
> Cheers.
>
>
> On 4 Jun 2013, at 11:35, "Chapman, Chris" <[log in to unmask]> wrote:
>
>> Hi FSL group,
>>
>> I am using setup_masks to block out lesions before randomise for TBSS. Are the input masks supposed to be in the format where 1=include (like the mean_FA_skeleton_mask) or the inverse? Sorry this wasn't clear from the documentation.
>>
>> Thank you,
>>
>> Chris Chapman
>> University of Michigan
>> Department of Radiation Oncology
>> Functional Imaging Group
>>
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 05:35:57 +0100
> From: Stephen Smith <[log in to unmask]>
> Subject: Re: Determining individual significance, if any, after group Melodic analysis
>
> Hi - it's not very clear what you're asking - but the standard way to do inference (thresholding) is not to look at the stage 2 outputs but to feed those into randomise. Any significant results across the group in the corrp image are significant for that group-level cross-subject model…. so you can't trivially separate that significant result out into individual subjects…..?
>
> Steve
>
>
>
> On 1 Jun 2013, at 16:46, Varina Wolf <[log in to unmask]> wrote:
>
>> Hello Experts,
>>
>> I’d like to determine which of my subjects show significant activation in the 3 ICs which withstood FWE correction (after group rs-fMRI analysis in Melodic followed by dual regression) in the corrp files followed by correction for multiple comparisons.
>>
>> I know that the individuals Z maps and ICs for every individual are in the dr_stage_2 files from dual regression (ie dr_stage2_ic0XXX and dr_subject0000X). I’ve been looking closely at these, and realize that it would be hard for me to say at what level I would threshold them to convince myself which of them actually has significant activity in the areas of the 3 ICs from group comparison. Am I way off here? Is this even possible? My goal is to look back and say, even if I was blinded from knowing which of these subjects has high or low IQ, I could look at these 3 ICs from that individual and make an educated guess, and be right more often than not. Or at least report how often I was wrong for the sake of showing what doesn’t work.
>>
>>
>> Thank you in advance,
>> Varina Wolf
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 05:37:21 +0100
> From: Stephen Smith <[log in to unmask]>
> Subject: Re: age as a regressor and age-group interaction term
>
> Hi - see the GLM page in the FSL wiki:
> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM
> Steve.
>
>
> On 1 Jun 2013, at 16:44, Varina Wolf <[log in to unmask]> wrote:
>
>> Hello experts,
>>
>> I've completed rs-fMRI analysis of my high and low IQ subjects in Melodic, all run together. I have set them up as one group in the GLM setup tool, with a contrast set between the high and low IQ groups.
>>
>> Now, too add age as a regressor, then I assume I can just add an EV and for each individual fill in their demeaned age, which for my group is between -7.4 and 12.9 years. Just to be sure, this is the correct way of handling this, right?
>>
>> Also, to test for any existing group-age interaction then is it correct to add 2 contrasts, such that there is a positive and a negative group-age interaction test, as shown below?
>>
>> /ContrasName1 high IQ>lowIQ /ContrastName2 hight IQ<low IQ
>> /ContrastName3 age-group-pos
>> /ContrastName4 age-group-neg
>> /NumWaves 3
>> /NumContrasts 4
>> /PPheights 1.615499e+00 1.615499e+00 2.347599e+01 2.347599e+01
>> /RequiredEffect 1.823 1.823 2.385 2.385
>>
>> /Matrix EV1 EV2 EV3
>> High>low IQ 1.000000e+00 -1.000000e+00 0.000000e+00
>> High<low IQ -1.000000e+00 1.000000e+00 0.000000e+00
>> Age-group pos 0.000000e+00 0.000000e+00 1.000000e+00
>> Age-group neg 0.000000e+00 0.000000e+00 -1.000000e+00
>>
>> Thank you for you help,
>> Varina Wolf, M.D.
>> Baylor College of Medicine
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 05:39:31 +0100
> From: Stephen Smith <[log in to unmask]>
> Subject: Re: Dual Regression, Image Exception : #22 :: ERROR, filenames can be basenames or not - RSVP
>
> Hi - if there is no output from stage 1 of dualreg then you need to look into the earlier log files than these!
> Cheers, Steve.
>
>
> On 1 Jun 2013, at 14:57, Saman Sarraf <[log in to unmask]> wrote:
>
>> Dear Dual Regression Experts,
>>
>> I have faced a bizarre problem in running my Dual Regression and appreciate if you can help me to solve it.
>> I get empty output from Dual Regression meaning that there is no stage 1 and 3 files.
>>
>> I followed up all suggestions on the JISCMAIL about the similar issue but I still have the same problem.
>>
>> This is the script I run for DR and I think there is no problem (as I used the same syntax and got results with other data)
>>
>> dual_regression /Users/samansarraf/Desktop/ADRS2mm.gica/groupmelodic.ica/melodic_IC 1 /Users/samansarraf/Desktop/AD_Matrix_Design/AD_Matrix_Design.mat /Users/samansarraf/Desktop/AD_Matrix_Design/AD_Matrix_Design.con 10000 DRADNEW `cat /Users/samansarraf/Desktop/ADRS2mm.gica/.filelist`
>>
>> I took a look at /Users/samansarraf/DRADNEW/scripts+logs/drD and it includes no error message and just includes (as an example):
>>
>> /Users/samansarraf/Downloads/FSL/fsl/bin/fslmerge -t DRADNEW/dr_stage2_ic0000 `$FSLDIR/bin/imglob DRADNEW/dr_stage2_subject*_ic0000.*` ; /Users/samansarraf/Downloads/FSL/fsl/bin/imrm `$FSLDIR/bin/imglob DRADNEW/dr_stage2_subject*_ic0000.*` ; /Users/samansarraf/Downloads/FSL/fsl/bin/randomise -i DRADNEW/dr_stage2_ic0000 -o DRADNEW/dr_stage3_ic0000 -m DRADNEW/mask -d /Users/samansarraf/Desktop/AD_Matrix_Design/AD_Matrix_Design.mat -t /Users/samansarraf/Desktop/AD_Matrix_Design/AD_Matrix_Design.con -n 10000 -T -V
>> ...
>>
>> Where ic0000 ends to ic0064.
>>
>> Then, I opened drD.exxxx.y files , and most of them have this error message:
>>
>> Image Exception : #22 :: ERROR: Could not open image DRADNEW/dr_stage2_ic000X(varies from 0 to 49 - # of components from MELODIC)
>> ERROR: Program failed
>>
>> An exception has been thrown
>> ERROR: Could not open image DRADNEW/dr_stage2_ic000X Trace: read_volume4DROI.
>>
>> Also, in the rest of files, I have this error:
>> Usage: /Users/samansarraf/Downloads/FSL/fsl/bin/imrm <list of image names to remove>
>> NB: filenames can be basenames or not
>> randomise options: -i DRADNEW/dr_stage2_ic00X -o DRADNEW/dr_stage3_ic00X -m DRADNEW/mask -d /Users/samansarraf/Desktop/AD_Matrix_Design/AD_Matrix_Design.mat -t /Users/samansarraf/Desktop/AD_Matrix_Design/AD_Matrix_Design.con -n 10000 -T -V
>> Loading Data:
>> (X goes from 0 to 49)
>> --------------------------------------------------------------------------------------------------
>> As I have a deadline in couple of days, I do appreciate if somebody can help in this matter.
>> PS: # of subjects = 50, RAM = 4 GB, PC = MAC Mini, OS X 10.8.3, Processor 2.5 GHz Intel Core i5, I used dcm2nii (Compressed FSL (4D NIfTI mii) to convert my DICOMs to NIfTI.
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 07:06:12 +0000
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: use of -usesqform
>
> Hi,
>
> I just thought I'd clarify the point about the NIFTI header a little.
>
> In FSL we do not, by default, use the full information about the NIFTI coordinate system (the qform and sform) but we _always_ preserve this information, transform it appropriately, and write it out. Furthermore, we do use the sign of the determinant of these matrices in order to determine the left/right order, and this is crucial. These matrices are not transformation matrices per se, but descriptions of coordinate systems and the qform usually contains the relationship between the voxel coordinates and the scanner coordinates. Almost all programs that create NIFTI files from other formats, such as DICOM, will populate the qform (and/or sform) with appropriate information. Whether this is useful for registration depends on if the scans are from the same session and the subject has not moved very much. Because the latter is not always known, we do not use the qform/sform by default and do not recommend it in all cases. However, for scans from the same session it can be useful as an initialisation.
>
> So, in summary, we do write this section on the NIFTI. We also rely upon the determinants. It is the DICOM to NIFTI conversion tools (or similar) that write the useful information into here. For registration, it can be useful as an initialisation if the scans are from the same session and there was no repositioning of the subject.
>
> All the best,
> Mark
>
>
> On 4 Jun 2013, at 13:09, Benjamin Kay <[log in to unmask]> wrote:
>
>> On Tuesday, June 04, 2013 05:30:24 you wrote:
>>> Hi
>>> i want to compute the linear transform between the diffusion space and my seed space which is freesurfer space (brain.mgz converted into nifti), my script is :
>>>
>>> flirt -in ~/dti50.bedpostX/nodif_brain -ref ~/ctr1_brain.nii.gz -omat /~dti50.bedpostX/xfms/diff2str.mat -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -cost corratio
>>>
>>> is it necessary to use 12 dof
>>
>> It sounds like you're going from one space/modality to another with the same brain. In that case, a 6 (rigid-body) or 7 (rigid-body + global scale) dof transform might be enough. Try it and see what works best for you.
>>
>>> and should i add the -usesqform option ?
>>
>> The NIFTI file format lets programs store transformation matrices in the NIFTI header. This helps to avoid multiple resampling and the accompanying artifacts. To my limited knowledge, fsl does not write to this section of the header. But if your NIFTI file came from a different program that uses this header (e.g. SPM), then you can to tell flirt to use that transformation matrix witht the -usesqform option.
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 08:50:06 +0100
> From: Chris Leatherday <[log in to unmask]>
> Subject: Nonlinear registration of atrophied brains
>
> Hello,
>
> I've been working on warping a group of elderly (Healthy control and Alzheimer's disease) brains to MNI space using FSL. I've got a T1 weighted MRI and an FDG-PET image for each subject, and I've been registering the data in accordance with the FNIRT user guide
>
> So my process has been:
>
> Use BET to extract the brain from the subject MRI
>
> Use FLIRT with dof 12 to register the brain extracted subject MRI to the 2mm brain extracted MNI template
>
> Use FNIRT in conjunction with the affine transform from the previous step to calculate a nonlinear warp to the 2mm MNI template. I was also using the config file T1_2_MNI152_2mm.cnf for FNIRT, but with no inmask specified.
>
> Use FLIRT with dof 6 to register the PET to the subject MRI
>
> Use ApplyWarp and the output from FNIRT to register the PET to MNI space.
>
> This works pretty well in most cases. When the reigstration didn't look great, I manually edited the brain masks from BET (in FSLview) so that they were more accurate, which improved the registration. I have also tried warping the betted subject brain image to the betted brain template, which again works pretty well for some of the 'troublesome' images. But there are still some that don't look great.
>
> I've read in a past post that lowering the warpres value for fnirt can improve the registration accuracy, particularly for atrophied and elderly brains. Is there anything else I can/should try to improve my registration? The problem is pretty much always with the grey matter, the subcortical structures register pretty well. The brains that won't warp well usually end up a bit squashed, particularly in the parietal lobe.
>
> Also, is there any reason I shouldn't register a brain extracted subject image to the brain extracted template? I figured this was okay as it's only the brain material I'm interested in anyway.
>
> Thank you
> Chris
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 09:51:55 +0100
> From: LAOUCHEDI MAKHLOUF <[log in to unmask]>
> Subject: FLIRT problem
>
> Hi
> i run flirt with 12 dof to register diffusion datasets to their T1 datasets and i noticed that for the brainstem (pons) the results are not as good as for the brain. does non linear (fnirt) improve the registration results ? or is there any other mean adapted for this purpose ?
>
> Thanks for help
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 10:14:28 +0100
> From: Stamatios Sotiropoulos <[log in to unmask]>
> Subject: Re: Number of no diffusion images for DTI and TBSS analyses
>
> Hi Giuseppe,
>
> It is no clear what you mean by "no diffusion image covering a direction".
>
> To fit the DTI model you need at least 6 diffusion-weighted images at a high b value (e.g. 1000 s/mm2) and different directions and one baseline image (normally obtained at b=0 s/mm2). If you have only one b=0 and one diffusion-weighted image, you cannot fit the tensor model that has 6 unknown parameters.
>
> Cheers
> Stam
>
>
>
> On 4 Jun 2013, at 21:43, giuseppe delvecchio wrote:
>
>> Dear FSL's users,
>> i am new with TBSS and DTI analyses and I would like to ask you a very basic question. In my DTI raw data I have only on no diffusion image (only one zero) covering only one direction. I have checked another sample of raw dti data and they have 7 no diffusion images covering 7 directions. I was wondering whether it is still possible to run a TBSS or a DTI analysis with only one no diffusion image? and most importantly, if it will give us significant results.
>> Thanks a lot,
>> Giuseppe
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 09:27:32 +0000
> From: Duncan Mortimer <[log in to unmask]>
> Subject: Re: I can not install FSL on mac 10.5.8 Quad-Core Intel Xeon
>
> Upgrade to a more recent (and supported) version of OS X. The minimum *we* currently support is 10.6.8 (but this is not officially supported by Apple), but I would *strongly* advise upgrading as far as allowed. The current release is 10.8 (with 10.9 likely to ship later this year) - note you would have to be running 10.6 to install 10.8 as it is only available through the Mac App Store.
>
> Duncan
> On 2 Jun 2013, at 18:18, Paulo Barraza wrote:
>
>> My problem is:
>>
>> I can not install FSL on Mac Pro 10.5.8 Quad-Core Intel Xeon.
>>
>> This is what appears on the terminal:
>>
>> ----------------
>>
>> 172-16-254-251: ~ paulobarraza $ cd ~ / Desktop
>> 172-16-254-251: $ python Desktop paulobarraza fslinstaller.py-- FSL Installer - Version 2.0.10 ---
>> [Warning] Some operations of the installer requires administative rights, for example installing into the default folder of / usr / local. If your account is an 'Administrator' (you have 'sudo' rights) then you will be PRompted for your administrator Password when necessary.
>> [OK] Installer is current
>> Where would you like to install FSL? [/ usr / local]:
>> [FAILED] This installer does not support this OS (apple darwin 9.8). Debian / Ubuntu users NeuroDebian Should look on the site for installation instructions.
>> 172-16-254-251: Desktop paulobarraza $
>>
>> ------------------------
>>
>> What should I do to solve this problem?
>>
>> I await your prompt response.
>>
>> Paulo B.
>
> --
> Duncan A B Mortimer DPhil MChem
> Computing Officer, FMRIB Centre, University of Oxford,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
> Tel: (0)1865 222713 email: [log in to unmask]
> Personal email (not for IT support): [log in to unmask]
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 10:42:30 +0100
> From: Jesper Andersson <[log in to unmask]>
> Subject: Re: Nonlinear registration of atrophied brains
>
> Dear Chris,
>
> when you say it doesn't look great, specifically what is the problem? Is it the final PET images or is it the structural MRIs after registration to the MNI?
>
> What one typically sees when registering atrophied brains with a 10mm warp resolution is that the resolution isn't quite enough and the widened sulci aren't "closed up" properly. It sounds like you are seeing something different?
>
> Jesper
>
> On 5 Jun 2013, at 08:50, Chris Leatherday wrote:
>
>> Hello,
>>
>> I've been working on warping a group of elderly (Healthy control and Alzheimer's disease) brains to MNI space using FSL. I've got a T1 weighted MRI and an FDG-PET image for each subject, and I've been registering the data in accordance with the FNIRT user guide
>>
>> So my process has been:
>>
>> Use BET to extract the brain from the subject MRI
>>
>> Use FLIRT with dof 12 to register the brain extracted subject MRI to the 2mm brain extracted MNI template
>>
>> Use FNIRT in conjunction with the affine transform from the previous step to calculate a nonlinear warp to the 2mm MNI template. I was also using the config file T1_2_MNI152_2mm.cnf for FNIRT, but with no inmask specified.
>>
>> Use FLIRT with dof 6 to register the PET to the subject MRI
>>
>> Use ApplyWarp and the output from FNIRT to register the PET to MNI space.
>>
>> This works pretty well in most cases. When the reigstration didn't look great, I manually edited the brain masks from BET (in FSLview) so that they were more accurate, which improved the registration. I have also tried warping the betted subject brain image to the betted brain template, which again works pretty well for some of the 'troublesome' images. But there are still some that don't look great.
>>
>> I've read in a past post that lowering the warpres value for fnirt can improve the registration accuracy, particularly for atrophied and elderly brains. Is there anything else I can/should try to improve my registration? The problem is pretty much always with the grey matter, the subcortical structures register pretty well. The brains that won't warp well usually end up a bit squashed, particularly in the parietal lobe.
>>
>> Also, is there any reason I shouldn't register a brain extracted subject image to the brain extracted template? I figured this was okay as it's only the brain material I'm interested in anyway.
>>
>> Thank you
>> Chris
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 10:48:55 +0100
> From: Jesper Andersson <[log in to unmask]>
> Subject: Re: topup function
>
> Dear Arnaud,
>
>> Thank you,removing the last slice in the z-direction was my "error". Finally, I was able to correct my b0 with applytopup. But now I want to use the information from topup to correct my DWI data and when I run :
>>
>> applytopup --imain=DWI.nii --datain=acquisition_parameters.txt --topup=my_topup_results --out=my_hifi_images_dwi --inindex=1
>>
>> I received this message: Invalid combination of phase-encode vectors for least-squares restoration.
>>
>> I tried to crop DWI.nii to have the same number of slice in z-direction that the b0.
>
> you definitely need to have the same number of slices for your dwis as for your b0.
>
>> I alse tried to change the acquisition_parameters.txt to : 0 1 0 0.0656
>
> The way you are calling applytopup you have specified a single --imain file, which tells applytopup that all images in that file has been acquired with the same acquisition parameters. If you have both blip-up and blip-down dwi images you need to split them into two files and do --imain=buDWI.nii,bdDWI.nii and then --inindex=1,2.
>
> If you truly have dwis acquired with the same acquisition parameters you need to use --method=jac as the default least-squares restoration relies on there being data with different distortions.
>
> Jesper
>
>
>>
>> But nothing works and I still have this error message.
>>
>> Thank for your help
>>
>> Arnaud
>>
>>
>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>> Yes,
>>
>> the problem here is with the odd number of slices which means it can't do the sub-sampling in the z-direction. What I usually recommend is to collect an even number of slices, and if not to delete one slice. Typically there will be one slice at the top or bottom that contain mostly air.
>>
>> Jesper
>>
>> On 4 Jun 2013, at 16:42, Arnaud Boré wrote:
>>
>>> Great
>>> Thank you Jesper !
>>> It almost works. Now I've got the error message : Topup: msg=topup_clp::topup_clp: Subsampling levels incompatible with image data.
>>>
>>> The 2 b0 are at the same resolution that my DWI's data and by default subsampling should be 1. I tried with 1,1,1 but then I've got this error : Topup: msg=topup_clp::topup_clp: Mismatch between --subsamp and other parameters.
>>>
>>> Could you help me with that.
>>>
>>> Thank you
>>> Arnaud
>>>
>>>
>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>> Hi there,
>>>
>>> > I'm trying to make topup function works but I run into a segmentation fault error.
>>> > I've got 2 b0 with a different Phase Encoding (P->A and A->P)
>>> >
>>> > I created the acquisition_parameters.txt file and like the user guide says I can put a 1 for the fourth column but it doesn't work.
>>> >
>>> > So here is my command line :
>>> >
>>> > topup --imain=b0s.nii --datain=acquisition_parameters.txt --out=my_topup_results
>>>
>>> add --config=b02b0.cnf to that
>>> >
>>> > My acquisition_parameters.txt file looks like this:
>>> >
>>> > 0 1 0 1
>>> > 0 -1 0 1
>>> >
>>> > In addition, I don't understand how to calculate the fourth column so here the parameters of my sequence. If somebody can explain me how to do that.
>>> >
>>> > TR = 9300ms , TE=94ms, Echo spacing = 0.69ms, 96x96 matrix and 65 slices,
>>> > Phase partial Fourier 6/8 and finally bandwidth 1628Hz/Px
>>>
>>> the relevant time in your case is (96-1)*0.00069 = 0.0656 seconds.
>>>
>>> Good luck Jesper
>>>
>>>
>>> >
>>> > Thank for your help
>>> >
>>> > Arnaud
>>>
>>>
>>>
>>> --
>>> Arnaud BORE
>>> Research assistant
>>> Cellulaire : (001) 514-647-8649
>>>
>>
>>
>>
>>
>> --
>> Arnaud BORE
>> Research assistant
>> Cellulaire : (001) 514-647-8649
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 10:50:59 +0100
> From: Jesper Andersson <[log in to unmask]>
> Subject: Re: FLIRT problem
>
> Dear Laouchedi,
>
>> i run flirt with 12 dof to register diffusion datasets to their T1 datasets and i noticed that for the brainstem (pons) the results are not as good as for the brain. does non linear (fnirt) improve the registration results ? or is there any other mean adapted for this purpose ?
>
> Fnirt often will improve that so I think that should be your first option to try.
>
> Jesper
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 11:16:53 +0100
> From: LAOUCHEDI MAKHLOUF <[log in to unmask]>
> Subject: Re: FLIRT problem
>
> Hi
> thank you Jesper for your reply, i have just to inform you that i will use the transformation matrix i produced using flirt (12 dof) between the diffusion space and the T1 space as an affine starting guess, but for the other parameters (subsamp, warpre, lambda ...), i want ask if you have an optimised script for such situations (registering diffusion volume of 256x256x56 to T1 256x256x256)
>
> Thanks a lot
>
> --- En date de : Mer 5.6.13, Jesper Andersson <[log in to unmask]> a écrit :
>
> De: Jesper Andersson <[log in to unmask]>
> Objet: Re: [FSL] FLIRT problem
> À: [log in to unmask]
> Date: Mercredi 5 juin 2013, 11h50
>
> Dear Laouchedi,
> i run flirt with 12 dof to register diffusion datasets to their T1 datasets and i noticed that for the brainstem (pons) the results are not as good as for the brain. does non linear (fnirt) improve the registration results ? or is there any other mean adapted for this purpose ?
>
> Fnirt often will improve that so I think that should be your first option to try.
> Jesper
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 11:23:22 +0100
> From: Jesper Andersson <[log in to unmask]>
> Subject: Re: FLIRT problem
>
> Hi again,
>
>> thank you Jesper for your reply, i have just to inform you that i will use the transformation matrix i produced using flirt (12 dof) between the diffusion space and the T1 space as an affine starting guess, but for the other parameters (subsamp, warpre, lambda ...), i want ask if you have an optimised script for such situations (registering diffusion volume of 256x256x56 to T1 256x256x256)
>>
>
> I'm sorry. I didn't read your original message carefully enough. I didn't realise you were registering diffusion to structural within same subject. My bad.
>
> In this situation my guess is that your problem is due to the distortions in the diffusion data. The brainstem can often be displaced quite a lot. The remedy for this is to either use a fieldmap (which means you need to have acquired one) or to use something like topup (which again means you must have acquired the right kind of data).
>
> Maybe Jon Brooks has some tips on what to do if you haven't acquired any of those as he has worked a lot with the brainstem. Jon?
>
> Jesper
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 18:28:34 +0800
> From: "Leatherday, Chris" <[log in to unmask]>
> Subject: Re: Nonlinear registration of atrophied brains
>
> Hi Jesper,
>
> Sorry, I wasn't clear enough in my description. The subject MRI doesn't register well to the template, the PET is then not registered well also, as it makes use of the same warp field through applywarp. Actually your description sounds pretty close, it's the outermost portion of grey matter that fails to register correctly in these cases. Perhaps using a 10mm warp resolution is insufficient? Also, is there any reason that registering the brain extracted subject MRI straight to the brain exctracted MNI template is not advisable?
>
> Cheers
> Chris
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Jesper Andersson
> Sent: Wed 6/5/2013 5:42 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Nonlinear registration of atrophied brains
>
> Dear Chris,
>
> when you say it doesn't look great, specifically what is the problem? Is it the final PET images or is it the structural MRIs after registration to the MNI?
>
> What one typically sees when registering atrophied brains with a 10mm warp resolution is that the resolution isn't quite enough and the widened sulci aren't "closed up" properly. It sounds like you are seeing something different?
>
> Jesper
>
> On 5 Jun 2013, at 08:50, Chris Leatherday wrote:
>
>> Hello,
>>
>> I've been working on warping a group of elderly (Healthy control and Alzheimer's disease) brains to MNI space using FSL. I've got a T1 weighted MRI and an FDG-PET image for each subject, and I've been registering the data in accordance with the FNIRT user guide
>>
>> So my process has been:
>>
>> Use BET to extract the brain from the subject MRI
>>
>> Use FLIRT with dof 12 to register the brain extracted subject MRI to the 2mm brain extracted MNI template
>>
>> Use FNIRT in conjunction with the affine transform from the previous step to calculate a nonlinear warp to the 2mm MNI template. I was also using the config file T1_2_MNI152_2mm.cnf for FNIRT, but with no inmask specified.
>>
>> Use FLIRT with dof 6 to register the PET to the subject MRI
>>
>> Use ApplyWarp and the output from FNIRT to register the PET to MNI space.
>>
>> This works pretty well in most cases. When the reigstration didn't look great, I manually edited the brain masks from BET (in FSLview) so that they were more accurate, which improved the registration. I have also tried warping the betted subject brain image to the betted brain template, which again works pretty well for some of the 'troublesome' images. But there are still some that don't look great.
>>
>> I've read in a past post that lowering the warpres value for fnirt can improve the registration accuracy, particularly for atrophied and elderly brains. Is there anything else I can/should try to improve my registration? The problem is pretty much always with the grey matter, the subcortical structures register pretty well. The brains that won't warp well usually end up a bit squashed, particularly in the parietal lobe.
>>
>> Also, is there any reason I shouldn't register a brain extracted subject image to the brain extracted template? I figured this was okay as it's only the brain material I'm interested in anyway.
>>
>> Thank you
>> Chris
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 07:09:10 -0400
> From: Arnaud Boré <[log in to unmask]>
> Subject: Re: topup function
>
> In fact all I've got just one 4D volume of DWI acquired with a phase
> encoding A->P (one b0 and 64 directions) and a pair of b0 acquired in both
> direction P->A and A->P.
> I thought that I could use the output information from topup with the b0s
> to correct my DWI runing applytopup.
>
> Can you tell me if it's possible ?
>
>
> 2013/6/5 Jesper Andersson <[log in to unmask]>
>
>> Dear Arnaud,
>>
>> Thank you,removing the last slice in the z-direction was my "error".
>> Finally, I was able to correct my b0 with applytopup. But now I want to use
>> the information from topup to correct my DWI data and when I run :
>>
>> applytopup --imain=DWI.nii --datain=acquisition_parameters.txt
>> --topup=my_topup_results --out=my_hifi_images_dwi --inindex=1
>>
>> I received this message: Invalid combination of phase-encode vectors for
>> least-squares restoration.
>>
>> I tried to crop DWI.nii to have the same number of slice in z-direction
>> that the b0.
>>
>>
>> you definitely need to have the same number of slices for your dwis as for
>> your b0.
>>
>> I alse tried to change the acquisition_parameters.txt to : 0 1 0 0.0656
>>
>>
>> The way you are calling applytopup you have specified a single --imain
>> file, which tells applytopup that all images in that file has been acquired
>> with the same acquisition parameters. If you have both blip-up and
>> blip-down dwi images you need to split them into two files and do
>> --imain=buDWI.nii,bdDWI.nii and then --inindex=1,2.
>>
>> If you truly have dwis acquired with the same acquisition parameters you
>> need to use --method=jac as the default least-squares restoration relies on
>> there being data with different distortions.
>>
>> Jesper
>>
>>
>>
>> But nothing works and I still have this error message.
>>
>> Thank for your help
>>
>> Arnaud
>>
>>
>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>
>>> Yes,
>>>
>>> the problem here is with the odd number of slices which means it can't do
>>> the sub-sampling in the z-direction. What I usually recommend is to collect
>>> an even number of slices, and if not to delete one slice. Typically there
>>> will be one slice at the top or bottom that contain mostly air.
>>>
>>> Jesper
>>>
>>> On 4 Jun 2013, at 16:42, Arnaud Boré wrote:
>>>
>>> Great
>>> Thank you Jesper !
>>> It almost works. Now I've got the error message : Topup:
>>> msg=topup_clp::topup_clp: Subsampling levels incompatible with image data.
>>>
>>> The 2 b0 are at the same resolution that my DWI's data and by default
>>> subsampling should be 1. I tried with 1,1,1 but then I've got this error
>>> : Topup: msg=topup_clp::topup_clp: Mismatch between --subsamp and other
>>> parameters.
>>>
>>> Could you help me with that.
>>>
>>> Thank you
>>> Arnaud
>>>
>>>
>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>>
>>>> Hi there,
>>>>
>>>> > I'm trying to make topup function works but I run into a segmentation
>>>> fault error.
>>>> > I've got 2 b0 with a different Phase Encoding (P->A and A->P)
>>>> >
>>>> > I created the acquisition_parameters.txt file and like the user guide
>>>> says I can put a 1 for the fourth column but it doesn't work.
>>>> >
>>>> > So here is my command line :
>>>> >
>>>> > topup --imain=b0s.nii --datain=acquisition_parameters.txt
>>>> --out=my_topup_results
>>>>
>>>> add --config=b02b0.cnf to that
>>>> >
>>>> > My acquisition_parameters.txt file looks like this:
>>>> >
>>>> > 0 1 0 1
>>>> > 0 -1 0 1
>>>> >
>>>> > In addition, I don't understand how to calculate the fourth column so
>>>> here the parameters of my sequence. If somebody can explain me how to do
>>>> that.
>>>> >
>>>> > TR = 9300ms , TE=94ms, Echo spacing = 0.69ms, 96x96 matrix and 65
>>>> slices,
>>>> > Phase partial Fourier 6/8 and finally bandwidth 1628Hz/Px
>>>>
>>>> the relevant time in your case is (96-1)*0.00069 = 0.0656 seconds.
>>>>
>>>> Good luck Jesper
>>>>
>>>>
>>>> >
>>>> > Thank for your help
>>>> >
>>>> > Arnaud
>>>>
>>>
>>>
>>>
>>> --
>>> Arnaud BORE
>>> Research assistant
>>> Cellulaire : (001) 514-647-8649
>>>
>>>
>>>
>>
>>
>> --
>> Arnaud BORE
>> Research assistant
>> Cellulaire : (001) 514-647-8649
>>
>>
>>
>
>
> --
> Arnaud BORE
> Research assistant
> Cellulaire : (001) 514-647-8649
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 12:11:18 +0100
> From: Jesper Andersson <[log in to unmask]>
> Subject: Re: topup function
>
> Hi again,
>
>> In fact all I've got just one 4D volume of DWI acquired with a phase encoding A->P (one b0 and 64 directions) and a pair of b0 acquired in both direction P->A and A->P.
>> I thought that I could use the output information from topup with the b0s to correct my DWI runing applytopup.
>>
>> Can you tell me if it's possible ?
>
> yes you can, but then you need to use the --method=jac switch.
>
> Jesper
>
>>
>>
>> 2013/6/5 Jesper Andersson <[log in to unmask]>
>> Dear Arnaud,
>>
>>> Thank you,removing the last slice in the z-direction was my "error". Finally, I was able to correct my b0 with applytopup. But now I want to use the information from topup to correct my DWI data and when I run :
>>>
>>> applytopup --imain=DWI.nii --datain=acquisition_parameters.txt --topup=my_topup_results --out=my_hifi_images_dwi --inindex=1
>>>
>>> I received this message: Invalid combination of phase-encode vectors for least-squares restoration.
>>>
>>> I tried to crop DWI.nii to have the same number of slice in z-direction that the b0.
>>
>> you definitely need to have the same number of slices for your dwis as for your b0.
>>
>>> I alse tried to change the acquisition_parameters.txt to : 0 1 0 0.0656
>>
>> The way you are calling applytopup you have specified a single --imain file, which tells applytopup that all images in that file has been acquired with the same acquisition parameters. If you have both blip-up and blip-down dwi images you need to split them into two files and do --imain=buDWI.nii,bdDWI.nii and then --inindex=1,2.
>>
>> If you truly have dwis acquired with the same acquisition parameters you need to use --method=jac as the default least-squares restoration relies on there being data with different distortions.
>>
>> Jesper
>>
>>
>>>
>>> But nothing works and I still have this error message.
>>>
>>> Thank for your help
>>>
>>> Arnaud
>>>
>>>
>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>> Yes,
>>>
>>> the problem here is with the odd number of slices which means it can't do the sub-sampling in the z-direction. What I usually recommend is to collect an even number of slices, and if not to delete one slice. Typically there will be one slice at the top or bottom that contain mostly air.
>>>
>>> Jesper
>>>
>>> On 4 Jun 2013, at 16:42, Arnaud Boré wrote:
>>>
>>>> Great
>>>> Thank you Jesper !
>>>> It almost works. Now I've got the error message : Topup: msg=topup_clp::topup_clp: Subsampling levels incompatible with image data.
>>>>
>>>> The 2 b0 are at the same resolution that my DWI's data and by default subsampling should be 1. I tried with 1,1,1 but then I've got this error : Topup: msg=topup_clp::topup_clp: Mismatch between --subsamp and other parameters.
>>>>
>>>> Could you help me with that.
>>>>
>>>> Thank you
>>>> Arnaud
>>>>
>>>>
>>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>>> Hi there,
>>>>
>>>> > I'm trying to make topup function works but I run into a segmentation fault error.
>>>> > I've got 2 b0 with a different Phase Encoding (P->A and A->P)
>>>> >
>>>> > I created the acquisition_parameters.txt file and like the user guide says I can put a 1 for the fourth column but it doesn't work.
>>>> >
>>>> > So here is my command line :
>>>> >
>>>> > topup --imain=b0s.nii --datain=acquisition_parameters.txt --out=my_topup_results
>>>>
>>>> add --config=b02b0.cnf to that
>>>> >
>>>> > My acquisition_parameters.txt file looks like this:
>>>> >
>>>> > 0 1 0 1
>>>> > 0 -1 0 1
>>>> >
>>>> > In addition, I don't understand how to calculate the fourth column so here the parameters of my sequence. If somebody can explain me how to do that.
>>>> >
>>>> > TR = 9300ms , TE=94ms, Echo spacing = 0.69ms, 96x96 matrix and 65 slices,
>>>> > Phase partial Fourier 6/8 and finally bandwidth 1628Hz/Px
>>>>
>>>> the relevant time in your case is (96-1)*0.00069 = 0.0656 seconds.
>>>>
>>>> Good luck Jesper
>>>>
>>>>
>>>> >
>>>> > Thank for your help
>>>> >
>>>> > Arnaud
>>>>
>>>>
>>>>
>>>> --
>>>> Arnaud BORE
>>>> Research assistant
>>>> Cellulaire : (001) 514-647-8649
>>>>
>>>
>>>
>>>
>>>
>>> --
>>> Arnaud BORE
>>> Research assistant
>>> Cellulaire : (001) 514-647-8649
>>>
>>
>>
>>
>>
>> --
>> Arnaud BORE
>> Research assistant
>> Cellulaire : (001) 514-647-8649
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 07:38:19 -0400
> From: Arnaud Boré <[log in to unmask]>
> Subject: Re: topup function
>
> Great !!
> Thank you very much Jesper for your help and all the explanations I really
> appreciated it !!!!
>
>
> 2013/6/5 Jesper Andersson <[log in to unmask]>
>
>> Hi again,
>>
>> In fact all I've got just one 4D volume of DWI acquired with a phase
>> encoding A->P (one b0 and 64 directions) and a pair of b0 acquired in both
>> direction P->A and A->P.
>> I thought that I could use the output information from topup with the b0s
>> to correct my DWI runing applytopup.
>>
>> Can you tell me if it's possible ?
>>
>>
>> yes you can, but then you need to use the --method=jac switch.
>>
>> Jesper
>>
>>
>>
>> 2013/6/5 Jesper Andersson <[log in to unmask]>
>>
>>> Dear Arnaud,
>>>
>>> Thank you,removing the last slice in the z-direction was my "error".
>>> Finally, I was able to correct my b0 with applytopup. But now I want to use
>>> the information from topup to correct my DWI data and when I run :
>>>
>>> applytopup --imain=DWI.nii --datain=acquisition_parameters.txt
>>> --topup=my_topup_results --out=my_hifi_images_dwi --inindex=1
>>>
>>> I received this message: Invalid combination of phase-encode vectors for
>>> least-squares restoration.
>>>
>>> I tried to crop DWI.nii to have the same number of slice in z-direction
>>> that the b0.
>>>
>>>
>>> you definitely need to have the same number of slices for your dwis as
>>> for your b0.
>>>
>>> I alse tried to change the acquisition_parameters.txt to : 0 1 0 0.0656
>>>
>>>
>>> The way you are calling applytopup you have specified a single --imain
>>> file, which tells applytopup that all images in that file has been acquired
>>> with the same acquisition parameters. If you have both blip-up and
>>> blip-down dwi images you need to split them into two files and do
>>> --imain=buDWI.nii,bdDWI.nii and then --inindex=1,2.
>>>
>>> If you truly have dwis acquired with the same acquisition parameters you
>>> need to use --method=jac as the default least-squares restoration relies on
>>> there being data with different distortions.
>>>
>>> Jesper
>>>
>>>
>>>
>>> But nothing works and I still have this error message.
>>>
>>> Thank for your help
>>>
>>> Arnaud
>>>
>>>
>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>>
>>>> Yes,
>>>>
>>>> the problem here is with the odd number of slices which means it can't
>>>> do the sub-sampling in the z-direction. What I usually recommend is to
>>>> collect an even number of slices, and if not to delete one slice. Typically
>>>> there will be one slice at the top or bottom that contain mostly air.
>>>>
>>>> Jesper
>>>>
>>>> On 4 Jun 2013, at 16:42, Arnaud Boré wrote:
>>>>
>>>> Great
>>>> Thank you Jesper !
>>>> It almost works. Now I've got the error message : Topup:
>>>> msg=topup_clp::topup_clp: Subsampling levels incompatible with image data.
>>>>
>>>> The 2 b0 are at the same resolution that my DWI's data and by default
>>>> subsampling should be 1. I tried with 1,1,1 but then I've got this error
>>>> : Topup: msg=topup_clp::topup_clp: Mismatch between --subsamp and other
>>>> parameters.
>>>>
>>>> Could you help me with that.
>>>>
>>>> Thank you
>>>> Arnaud
>>>>
>>>>
>>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>>>
>>>>> Hi there,
>>>>>
>>>>> > I'm trying to make topup function works but I run into a segmentation
>>>>> fault error.
>>>>> > I've got 2 b0 with a different Phase Encoding (P->A and A->P)
>>>>> >
>>>>> > I created the acquisition_parameters.txt file and like the user guide
>>>>> says I can put a 1 for the fourth column but it doesn't work.
>>>>> >
>>>>> > So here is my command line :
>>>>> >
>>>>> > topup --imain=b0s.nii --datain=acquisition_parameters.txt
>>>>> --out=my_topup_results
>>>>>
>>>>> add --config=b02b0.cnf to that
>>>>> >
>>>>> > My acquisition_parameters.txt file looks like this:
>>>>> >
>>>>> > 0 1 0 1
>>>>> > 0 -1 0 1
>>>>> >
>>>>> > In addition, I don't understand how to calculate the fourth column so
>>>>> here the parameters of my sequence. If somebody can explain me how to do
>>>>> that.
>>>>> >
>>>>> > TR = 9300ms , TE=94ms, Echo spacing = 0.69ms, 96x96 matrix and 65
>>>>> slices,
>>>>> > Phase partial Fourier 6/8 and finally bandwidth 1628Hz/Px
>>>>>
>>>>> the relevant time in your case is (96-1)*0.00069 = 0.0656 seconds.
>>>>>
>>>>> Good luck Jesper
>>>>>
>>>>>
>>>>> >
>>>>> > Thank for your help
>>>>> >
>>>>> > Arnaud
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Arnaud BORE
>>>> Research assistant
>>>> Cellulaire : (001) 514-647-8649
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Arnaud BORE
>>> Research assistant
>>> Cellulaire : (001) 514-647-8649
>>>
>>>
>>>
>>
>>
>> --
>> Arnaud BORE
>> Research assistant
>> Cellulaire : (001) 514-647-8649
>>
>>
>>
>
>
> --
> Arnaud BORE
> Research assistant
> Cellulaire : (001) 514-647-8649
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 13:54:46 +0200
> From: maria estanqueiro <[log in to unmask]>
> Subject: Re: FLIRT problem
>
> Hi,
>
> I'm sorry for the intrusion but I have a question related to applying Flirt
> to corregister a FA image to a T1 within the same subject.
>
> Is there any recommendation on how to do this? For example which are the
> best options of cost function and interpolation?
>
> I have been playing around a bit with these options and it's still not
> clear to me..
>
> Thanks a lot
>
>
> 2013/6/5 Jesper Andersson <[log in to unmask]>
>
>> Hi again,
>>
>> thank you Jesper for your reply, i have just to inform you that i will
>> use the transformation matrix i produced using flirt (12 dof) between the
>> diffusion space and the T1 space as an affine starting guess, but for the
>> other parameters (subsamp, warpre, lambda ...), i want ask if you have an
>> optimised script for such situations (registering diffusion volume of
>> 256x256x56 to T1 256x256x256)
>>
>>
>> I'm sorry. I didn't read your original message carefully enough. I didn't
>> realise you were registering diffusion to structural within same subject.
>> My bad.
>>
>> In this situation my guess is that your problem is due to the distortions
>> in the diffusion data. The brainstem can often be displaced quite a lot.
>> The remedy for this is to either use a fieldmap (which means you need to
>> have acquired one) or to use something like topup (which again means you
>> must have acquired the right kind of data).
>>
>> Maybe Jon Brooks has some tips on what to do if you haven't acquired any
>> of those as he has worked a lot with the brainstem. Jon?
>>
>> Jesper
>>
>>
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 10:05:37 -0400
> From: Satrajit Ghosh <[log in to unmask]>
> Subject: Re: segfault from betting
>
>> Hi - FSL has never allowed NaNs - they can be removed using fslmaths.
>>
>
> thanks steve, i did that.
>
> my surprise was that while bet segfaulted, fslview did fine loading the
> file with nans. (so perhaps not all of fsl :) )
>
> cheers,
>
> satra
>
> On 5 Jun 2013, at 03:11, Satrajit Ghosh <[log in to unmask]> wrote:
>>
>> found the issue - the file had nans in it. perhaps that could be tested
>> during read.
>>
>> cheers,
>>
>> satra
>>
>> On Tue, Jun 4, 2013 at 9:40 PM, Satrajit Ghosh <[log in to unmask]> wrote:
>>
>>> hi all,
>>>
>>> i'm running into a segfault trying to bet this file. any thoughts?
>>>
>>> https://dl.dropboxusercontent.com/u/363467/mean_cannot_bet.nii.gz
>>>
>>> cheers,
>>>
>>> satra
>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>> Stop the cultural destruction of Tibet <http://smithinks.net>
>>
>>
>>
>>
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 15:08:07 +0100
> From: Stephen Smith <[log in to unmask]>
> Subject: Re: segfault from betting
>
>
> On 5 Jun 2013, at 15:05, Satrajit Ghosh <[log in to unmask]> wrote:
>
>>
>> Hi - FSL has never allowed NaNs - they can be removed using fslmaths.
>>
>> thanks steve, i did that.
>>
>> my surprise was that while bet segfaulted, fslview did fine loading the file with nans.
>
> that must be because fslview is more fully open source...
>
>
>> (so perhaps not all of fsl :) )
>>
>> cheers,
>>
>> satra
>>
>> On 5 Jun 2013, at 03:11, Satrajit Ghosh <[log in to unmask]> wrote:
>>
>>> found the issue - the file had nans in it. perhaps that could be tested during read.
>>>
>>> cheers,
>>>
>>> satra
>>>
>>> On Tue, Jun 4, 2013 at 9:40 PM, Satrajit Ghosh <[log in to unmask]> wrote:
>>> hi all,
>>>
>>> i'm running into a segfault trying to bet this file. any thoughts?
>>>
>>> https://dl.dropboxusercontent.com/u/363467/mean_cannot_bet.nii.gz
>>>
>>> cheers,
>>>
>>> satra
>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>> Stop the cultural destruction of Tibet
>>
>>
>>
>>
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 10:12:31 -0400
> From: Supreet kaur <[log in to unmask]>
> Subject: TBSS reregistration
>
> Dear FSL experts,
>
> I am new to the TBSS. I just conducted the second step of the TBSS
> registration, however,
> after the registration no stat folder was created and it seem to have
> stopped .
> Also I wanted to use my own target image for neonatal brains.
>
> I'll appreciate your feedback on this.
>
> [fsl@localhost mytbss]$ tbss_2_reg
>
> Usage: tbss_2_reg [options]
>
> Target-selection options - choose ONE of:
> -T : use FMRIB58_FA_1mm as target for nonlinear registrations
> (recommended)
> -t <target> : use <target> image as target for nonlinear registrations
> -n : find best target from all images in FA
>
> [fsl@localhost mytbss]$ tbss_2_reg -T
> 81101-Image-FA_FA_to_target
> 81141-Image-FA_FA_to_target
> 81391-Image-FA_FA_to_target
> 81761-Image-FA_FA_to_target
> 82391-Image-FA_FA_to_target
> 82461-Image-FA_FA_to_target
> 82681-Image-FA_FA_to_target
> 82711-Image-FA_FA_to_target
> 82821-Image-FA_FA_to_target
> 83121-Image-FA_FA_to_target
> 83221-Image-FA_FA_to_target
> 83231-Image-FA_FA_to_target
> 83501-Image-FA_FA_to_target
> 83562-Image-FA_FA_to_target
> 83671-Image-FA_FA_to_target
> 83681-Image-FA_FA_to_target
> 83841-Image-FA_FA_to_target
> 83871-Image-FA_FA_to_target
> 84251-Image-FA_FA_to_target
> 84281-Image-FA_FA_to_target
> 84481-Image-FA_FA_to_target
> D10051-Image-FA_FA_to_target
> Target_FA_to_target
>
>
> Thanks in advance,
>
> Sincerely,
>
> Supreet
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 16:16:37 +0200
> From: Rosalia Dacosta Aguayo <[log in to unmask]>
> Subject: Re: TBSS reregistration
>
> Hi Supreet,
>
> With second step there is no stat folder. You should have mytbss folder and
> another folder with origdata....
>
> With this information is difficult to understand what it is happening with
> your data.
>
> I recommend you read fslwiki about tbss process.
>
> Kind regards,
> Rosalia.
>
> 2013/6/5 Supreet kaur <[log in to unmask]>
>
>> Dear FSL experts,
>>
>> I am new to the TBSS. I just conducted the second step of the TBSS
>> registration, however,
>> after the registration no stat folder was created and it seem to have
>> stopped .
>> Also I wanted to use my own target image for neonatal brains.
>>
>> I'll appreciate your feedback on this.
>>
>> [fsl@localhost mytbss]$ tbss_2_reg
>>
>> Usage: tbss_2_reg [options]
>>
>> Target-selection options - choose ONE of:
>> -T : use FMRIB58_FA_1mm as target for nonlinear registrations
>> (recommended)
>> -t <target> : use <target> image as target for nonlinear registrations
>> -n : find best target from all images in FA
>>
>> [fsl@localhost mytbss]$ tbss_2_reg -T
>> 81101-Image-FA_FA_to_target
>> 81141-Image-FA_FA_to_target
>> 81391-Image-FA_FA_to_target
>> 81761-Image-FA_FA_to_target
>> 82391-Image-FA_FA_to_target
>> 82461-Image-FA_FA_to_target
>> 82681-Image-FA_FA_to_target
>> 82711-Image-FA_FA_to_target
>> 82821-Image-FA_FA_to_target
>> 83121-Image-FA_FA_to_target
>> 83221-Image-FA_FA_to_target
>> 83231-Image-FA_FA_to_target
>> 83501-Image-FA_FA_to_target
>> 83562-Image-FA_FA_to_target
>> 83671-Image-FA_FA_to_target
>> 83681-Image-FA_FA_to_target
>> 83841-Image-FA_FA_to_target
>> 83871-Image-FA_FA_to_target
>> 84251-Image-FA_FA_to_target
>> 84281-Image-FA_FA_to_target
>> 84481-Image-FA_FA_to_target
>> D10051-Image-FA_FA_to_target
>> Target_FA_to_target
>>
>>
>> Thanks in advance,
>>
>> Sincerely,
>>
>> Supreet
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 10:17:43 -0400
> From: Satrajit Ghosh <[log in to unmask]>
> Subject: Re: segfault from betting
>
>> that must be because fslview is more fully open source...
>>
>
> :)
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 16:23:00 +0100
> From: JISCMail Helpline <[log in to unmask]>
> Subject: Message from JISCMail Helpline: lists with public archives
>
> Dear subscribers
>
> We've had a lot of queries recently about the availability and visibility of JISCMail list archives in Google.
>
> This is just a reminder that messages sent to a list with public archives will be available to anyone on the internet.
>
> Your email will not be visible to non-subscribers, but remember if you reply to the list there may be information in your message which will be visible, such as your signature or attachments.
>
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>
> We hope this makes the situation clearer.
>
>
> Lisa
>
> --
> Lisa Vincent
>
> Operations Manager
> [log in to unmask]
> 0191 222 8179
>
> JISCMail is a JISC Advance Service
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 11:50:14 -0400
> From: Gonzalo Rojas Costa <[log in to unmask]>
> Subject: sienax with betted image...
>
> Hi:
>
> How can I use sienax with a betted image ?...
>
> Sincerely,
>
>
>
> --
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 17:55:13 +0200
> From: Elena Molina <[log in to unmask]>
> Subject: design.mat & design.com in randomise
>
> Dear all,
>
> I am running a rsfMRI analysis (3 different groups) and I have some
> questions about the randomise tool. Do I have to use the
> exchangeability-block (design.grp) file?
>
> I created the design and contrast matrix but I am also confused about
> covariates and demeaning.I have 3EV's (one per group) and 2EV's (age &
> gender). I demeaned the age and gender regressors. Is it correct?
>
> I attached the design.mat/design.con/design.grp flies. Can someone ckeck
> them? Thanks in advance.
>
> Best regards,
> Elena
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 09:00:28 -0700
> From: Dianne Patterson <[log in to unmask]>
> Subject: Re: topup function
>
> If I understand this exchange correctly, there are 2 variations for using
> topup/applytopup:
>
> 1) acquire B0+4d volume of DWI blip-up AND
> acquire B0+4d volume of DWI blip down
> (then topup, applytopup)
>
> OR
>
> 2) acquire a B0 only blip-up AND
> acquire B0+4d volume of DWI blip down
> (then topup, applytopup)
>
> Given that both #1 and #2 work with topup/applytopup, and that #1
> takes nearly twice as long to acquire...are there any benefits to #1
> over #2 (or is #1 simply a waste of scan time)?
>
> Thankyou,
>
> -Dianne
>
>
> On Wed, Jun 5, 2013 at 4:11 AM, Jesper Andersson <[log in to unmask]>wrote:
>
>> Hi again,
>>
>> In fact all I've got just one 4D volume of DWI acquired with a phase
>> encoding A->P (one b0 and 64 directions) and a pair of b0 acquired in both
>> direction P->A and A->P.
>> I thought that I could use the output information from topup with the b0s
>> to correct my DWI runing applytopup.
>>
>> Can you tell me if it's possible ?
>>
>>
>> yes you can, but then you need to use the --method=jac switch.
>>
>> Jesper
>>
>>
>>
>> 2013/6/5 Jesper Andersson <[log in to unmask]>
>>
>>> Dear Arnaud,
>>>
>>> Thank you,removing the last slice in the z-direction was my "error".
>>> Finally, I was able to correct my b0 with applytopup. But now I want to use
>>> the information from topup to correct my DWI data and when I run :
>>>
>>> applytopup --imain=DWI.nii --datain=acquisition_parameters.txt
>>> --topup=my_topup_results --out=my_hifi_images_dwi --inindex=1
>>>
>>> I received this message: Invalid combination of phase-encode vectors for
>>> least-squares restoration.
>>>
>>> I tried to crop DWI.nii to have the same number of slice in z-direction
>>> that the b0.
>>>
>>>
>>> you definitely need to have the same number of slices for your dwis as
>>> for your b0.
>>>
>>> I alse tried to change the acquisition_parameters.txt to : 0 1 0 0.0656
>>>
>>>
>>> The way you are calling applytopup you have specified a single --imain
>>> file, which tells applytopup that all images in that file has been acquired
>>> with the same acquisition parameters. If you have both blip-up and
>>> blip-down dwi images you need to split them into two files and do
>>> --imain=buDWI.nii,bdDWI.nii and then --inindex=1,2.
>>>
>>> If you truly have dwis acquired with the same acquisition parameters you
>>> need to use --method=jac as the default least-squares restoration relies on
>>> there being data with different distortions.
>>>
>>> Jesper
>>>
>>>
>>>
>>> But nothing works and I still have this error message.
>>>
>>> Thank for your help
>>>
>>> Arnaud
>>>
>>>
>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>>
>>>> Yes,
>>>>
>>>> the problem here is with the odd number of slices which means it can't
>>>> do the sub-sampling in the z-direction. What I usually recommend is to
>>>> collect an even number of slices, and if not to delete one slice. Typically
>>>> there will be one slice at the top or bottom that contain mostly air.
>>>>
>>>> Jesper
>>>>
>>>> On 4 Jun 2013, at 16:42, Arnaud Boré wrote:
>>>>
>>>> Great
>>>> Thank you Jesper !
>>>> It almost works. Now I've got the error message : Topup:
>>>> msg=topup_clp::topup_clp: Subsampling levels incompatible with image data.
>>>>
>>>> The 2 b0 are at the same resolution that my DWI's data and by default
>>>> subsampling should be 1. I tried with 1,1,1 but then I've got this error
>>>> : Topup: msg=topup_clp::topup_clp: Mismatch between --subsamp and other
>>>> parameters.
>>>>
>>>> Could you help me with that.
>>>>
>>>> Thank you
>>>> Arnaud
>>>>
>>>>
>>>> 2013/6/4 Jesper Andersson <[log in to unmask]>
>>>>
>>>>> Hi there,
>>>>>
>>>>> > I'm trying to make topup function works but I run into a segmentation
>>>>> fault error.
>>>>> > I've got 2 b0 with a different Phase Encoding (P->A and A->P)
>>>>> >
>>>>> > I created the acquisition_parameters.txt file and like the user guide
>>>>> says I can put a 1 for the fourth column but it doesn't work.
>>>>> >
>>>>> > So here is my command line :
>>>>> >
>>>>> > topup --imain=b0s.nii --datain=acquisition_parameters.txt
>>>>> --out=my_topup_results
>>>>>
>>>>> add --config=b02b0.cnf to that
>>>>> >
>>>>> > My acquisition_parameters.txt file looks like this:
>>>>> >
>>>>> > 0 1 0 1
>>>>> > 0 -1 0 1
>>>>> >
>>>>> > In addition, I don't understand how to calculate the fourth column so
>>>>> here the parameters of my sequence. If somebody can explain me how to do
>>>>> that.
>>>>> >
>>>>> > TR = 9300ms , TE=94ms, Echo spacing = 0.69ms, 96x96 matrix and 65
>>>>> slices,
>>>>> > Phase partial Fourier 6/8 and finally bandwidth 1628Hz/Px
>>>>>
>>>>> the relevant time in your case is (96-1)*0.00069 = 0.0656 seconds.
>>>>>
>>>>> Good luck Jesper
>>>>>
>>>>>
>>>>> >
>>>>> > Thank for your help
>>>>> >
>>>>> > Arnaud
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Arnaud BORE
>>>> Research assistant
>>>> Cellulaire : (001) 514-647-8649
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Arnaud BORE
>>> Research assistant
>>> Cellulaire : (001) 514-647-8649
>>>
>>>
>>>
>>
>>
>> --
>> Arnaud BORE
>> Research assistant
>> Cellulaire : (001) 514-647-8649
>>
>>
>>
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> [log in to unmask] <[log in to unmask]>
> or
> [log in to unmask]
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> (Just East of Harvill)
> 621-9877
> ==============
> "If you have an apple and I have an apple and we exchange these apples then
> you and I will still each have one apple. But if you have an idea and I
> have an idea and we exchange these ideas, then each of us will have two
> ideas." - George Bernard Shaw
> ==============
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 17:17:33 +0100
> From: Mark <[log in to unmask]>
> Subject: cluster command question
>
> Hi,
>
> I've searched the archive still can't figure out the problem I encountered. I know that by default only 6 local maxima (LM) are reported per cluster. In one of my contrast (thresholded at z=2.0), I identified one big cluster, and Firefox reported 6 LMs:
>
> Cluster Index Z x y z
> 1 3.59 4 -64 48
> 1 2.69 10 -52 40
> 1 2.63 4 -46 46
> 1 2.54 10 -70 44
> 1 2.52 0 -76 38
> 1 2.51 18 -74 42
>
> I's like to get more LMs within this cluster. So I performed "cluster -i cope.feat/thresh_zstat1.nii.gz -t 2.0 -n 10 --mm" and the results were:
>
> Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm)
> 1 896 3.59 4 -64 48 5.76 -64 43.7
>
> Why only one LM was yielded?
>
> Thanks in advance.
>
> Mark
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 17:23:14 +0100
> From: Tony Jiang <[log in to unmask]>
> Subject: beta series correlation
>
> Dear All,
>
> I was wondering if there is a quick dirty trick to run beta series correlation in Feat. My data has over 100 trials so I am trying to get an estimate of 100+ betas for each trial. but setting this up in Feat seems to overwhelm the GUI? I can create the .fsf file using scripts then if I load it to Feat GUI, it will take forever to load the model if i click on Full Model Setup.
>
> any suggestions are welcome!
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 17:48:28 +0100
> From: SUBSCRIBE FSL Jay <[log in to unmask]>
> Subject: FDT registration
>
> Hello,
>
> I am trying to create the linear and non-linear transformations for the diffusion data to standard space (MNI152_T1_1mm) using structural anatomic data. I used the Registration tab to get these transformations.
>
> I see that the following log when i do that (pasted below). Why is it that T1_2_MNI152_2mm configuration file being used for fnirt (anatomical to standard) and convertwarp (diff2standard_warp) uses MNI152_T1_2mm reference, even though i chose MNI152_T1_1mm standard space for registration. Wouldnt it go wrong when the fibers are binned in 1mm standard space(using seeds in 1mm standard space) and the transformations that are used, are from 2mm standard space?
>
> coordinate space Aligned Anatomical
>
> Regards
> Jay
> ====================================
> /user/local/jay/fsl/bin/flirt -in /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/nodif_brain -ref /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/anat_${name}.nii.gz -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6 -cost corratio -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str
>
> /user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2diff.mat -inverse /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat
>
> /user/local/jay/fsl/bin/flirt -in /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/anat_${name}.nii.gz -ref /user/local/jay/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -cost corratio -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard
>
> /user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2str.mat -inverse /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat
>
> /user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2standard.mat -concat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat
>
> /user/local/jay/fsl/bin/convert_xfm -omat /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2diff.mat -inverse /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2standard.mat
>
> /user/local/jay/fsl/bin/fnirt --in=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/anat_${name}_struc_cut.nii.gz --aff=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard.mat --cout=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_warp --config=T1_2_MNI152_2mm --iout=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_fnirt
>
> /user/local/jay/fsl/bin/invwarp -w /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_warp -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2str_warp -r /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/nodif_brain_mask
>
> /user/local/jay/fsl/bin/convertwarp -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2standard_warp -r /user/local/jay/fsl/data/standard/MNI152_T1_2mm -m /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/diff2str.mat -w /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2standard_warp
>
> /user/local/jay/fsl/bin/convertwarp -o /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2diff_warp -r /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/nodif_brain_mask -w /Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/standard2str_warp --postmat=/Space/jay/DTI_PWD_baseline_JA_bedpostX/${name}.bedpostX/xfms/str2diff.mat
> ====================================
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 17:00:08 +0000
> From: "Harms, Michael" <[log in to unmask]>
> Subject: Re: beta series correlation
>
> If you can create the .fsf file using scripts, then just skip the Feat GUI
> entirely and run
> feat design.fsf
> at the command line.
>
> cheers,
> -MH
> --
> Michael Harms, Ph.D.
>
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: [log in to unmask]
>
>
>
>
> On 6/5/13 11:23 AM, "Tony Jiang" <[log in to unmask]> wrote:
>
>>Dear All,
>>
>>I was wondering if there is a quick dirty trick to run beta series
>>correlation in Feat. My data has over 100 trials so I am trying to get
>>an estimate of 100+ betas for each trial. but setting this up in Feat
>>seems to overwhelm the GUI? I can create the .fsf file using scripts then
>>if I load it to Feat GUI, it will take forever to load the model if i
>>click on Full Model Setup.
>>
>>any suggestions are welcome!
>
>
> ________________________________
> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 17:05:08 +0000
> From: "Ackerman, JosephJr." <[log in to unmask]>
> Subject: Re: Neonatal TBSS
>
> Hello Supreet.
>
> I also used TBSS on neonatal brains and found that fsl_reg (with the -FA option) did a poor job since it assumes adult parameters. I had to rewrite the tbss steps 1-3 in order to get more reliable registration for linear and non-linear fits. I basically removed the fsl_reg part and inserted a triple step of flirt, fnirt and applywarp (which is what fsl_reg employees). I also built in an option to not use and atlas space at all and stay in target space so as not to resample the data again. For the global measures I was looking at I saw no real difference when not transforming the data from native, to target or native, to target, to atlas.
>
> The results seem to be working well.
>
> As well I did my alignments and transformations on the frame1 (the b0 volume(s)) from my subjects and then applied those matrix transformations to the FA volumes. For my subjects the FA volumes were not the easiest to align when using only them.
>
> Hope this helps in a little way. It can be done.
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Supreet kaur
> Sent: Tuesday, June 04, 2013 11:03 AM
> To: [log in to unmask]
> Subject: [FSL] Neonatal TBSS
>
> Dear FSL experts,
> I am trying to analyze the TBSS in neonatal brains .However, the standard space used for the non-linear registeration of FA maps, does not seem to be working well:
>
> Is someone working with the neonatal brain images for the TBSS.
> I'd appreciate your response.
> Thanks in advance.
>
> Sincerely,
>
> Supreet
>
>
> ________________________________
>
> The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 19:22:23 +0200
> From: Ahmad Omar <[log in to unmask]>
> Subject: Re: Resting state fMRI using MELODIC
>
> Hi Steve,
>
> Would you please send me the web page address to upload a data set for you
> to look at?
>
> Thanks for your assistance.
> Ahmad
>
> Ahmad Omar
>
>
>
> On Mon, Jun 3, 2013 at 5:44 PM, Ahmad Omar <[log in to unmask]> wrote:
>
>> Hi Christian,
>>
>> Would you please send me the web page address to upload a data set for you
>> to look at?
>>
>> Thanks for your assistance.
>> Ahmad
>>
>> Ahmad Omar
>>
>>
>>
>> On Fri, May 31, 2013 at 9:10 PM, Ahmad Omar <[log in to unmask]> wrote:
>>
>>> Hi Christian,
>>>
>>> The runs we have been doing have been on a single subject. You suspect
>>> that the data set is bad, right? I will try to upload it from the center.
>>>
>>> Thanks for your help.
>>> Ahmad
>>>
>>> Ahmad Omar
>>>
>>>
>>>
>>> On Fri, May 31, 2013 at 8:56 AM, Christian F. Beckmann <
>>> [log in to unmask]> wrote:
>>>
>>>> Hi,
>>>>
>>>> I suggest running single-subject ICAs first, just to see if the data
>>>> quality per se is OK or if you happen to have strange artefacts in your
>>>> data. If you cannot make this work then feel free to upload a single data
>>>> set so we can see what's going on...
>>>>
>>>> hth
>>>> Christian
>>>>
>>>>
>>>>
>>>> On 31 May 2013, at 11:53, Ahmad Omar <[log in to unmask]> wrote:
>>>>
>>>> > Hi Steve,
>>>> >
>>>> > Thank you for your reply. Unfortunately, we are only getting what in
>>>> some places are randomly scattered activations in the midbrain or
>>>> concentrated activations in the frontal and orbito-frontal regions where
>>>> there is already some epi-related distortions so not be relied upon . I
>>>> was meaning to ask this follow-up question. Shouldn't I turn off temporal
>>>> high pass filtering as I am interested in the ultra-low frequency BOLD
>>>> > signals? I tried a run doing that and the activation areas changed a
>>>> bit to being around the ventricles and in the putamen which also looked
>>>> strange to us.
>>>> >
>>>> > We very much appreciate your help on this.
>>>> >
>>>> > Ahmad
>>>> >
>>>> > Ahmad Omar
>>>> >
>>>> >
>>>> >
>>>> > On Thu, May 30, 2013 at 1:00 AM, Stephen Smith <[log in to unmask]>
>>>> wrote:
>>>> > Hi - there's nothing in this description or the log that jumps out at
>>>> me - did you find *some* RSNs that you recognised?
>>>> > Steve.
>>>> >
>>>> > On 29 May 2013, at 16:31, Ahmad Omar <[log in to unmask]> wrote:
>>>> >
>>>> >>
>>>> >> Re-send. Thanks.
>>>> >>
>>>> >>
>>>> >> Ahmad Omar
>>>> >>
>>>> >>
>>>> >>
>>>> >> ---------- Forwarded message ----------
>>>> >> From: Ahmad Omar <[log in to unmask]>
>>>> >> Date: Mon, May 27, 2013 at 4:53 PM
>>>> >> Subject: Resting state fMRI using MELODIC
>>>> >> To: FSL Mailing List <[log in to unmask]>
>>>> >>
>>>> >>
>>>> >> Hello All,
>>>> >>
>>>> >> I am trying to apply MELODIC (ver. 3.13, FSL ver 5.0.4 on a virtual
>>>> machine) to some resting-state fMRI data we are acquiring here at the
>>>> radiology center. The scanner is a 3T Siemens Skyra. The sequence is the
>>>> standard ep2d sequence acquiring 150 time points with TR = 2.57 sec, TE =
>>>> 36 msec, flip angle = 75 deg, distance factor = 20, PAT = 2, Fat Sat. on,
>>>> phase partial Fourier off, bandwidth = 1698 Hz/Px and 1.7mm x 1.7 mm x 5 mm
>>>> (in the z-axis direction) resolution with interleaved slice acquisition.
>>>> Motion correction and temporal high pass filtering were enabled in the
>>>> scanner sequence. When I view and loop through the raw data in FSL View, it
>>>> seems fine. No excessive translations or head rotation and no severe
>>>> intensity variations. In MELODIC I set the following settings: Delete
>>>> Volumes = 3, High pass filter cutoff (s) = 100, Motion Correction :
>>>> MCFLIRT, Slice timing correction: Interleaved, spatial smoothing FWHM (mm)
>>>> = 5, Temporal filtering: Highpass, Threshold IC maps left at 0.5 and
>>>> output the full stats folder was enabled. We were trying to reproduce the
>>>> work done by Tang, L et al. in the paper "Thalamic Resting-State
>>>> Functional Networks: Disruption in Patients with Mild Traumatic Brain
>>>> Injury". MELODIC finishes processing fine but we don't know why we are not
>>>> seeing any meaningful activations in say the Default Mode Network areas let
>>>> alone activations in the thalamus. I have included below a part of the
>>>> log.txt file in the filtered_func_data.ica folder.
>>>> >>
>>>> >> Thanks and your help is much appreciated.
>>>> >>
>>>> >> Melodic Version 3.13
>>>> >>
>>>> >> /usr/local/fsl/bin/melodic -i filtered_func_data -o
>>>> filtered_func_data.ica -v --nobet --bgthreshold=3 --tr=2.5699999332
>>>> --report --guireport=../../report.html -d 0 --mmthresh=0.5 --Ostats
>>>> >> ---------------------------------------------
>>>> >>
>>>> >> Melodic results will be in filtered_func_data.ica
>>>> >>
>>>> >> Create mask ... done
>>>> >> Reading data file filtered_func_data ... done
>>>> >> Estimating data smoothness ... done
>>>> >> Removing mean image ... done
>>>> >> Normalising by voxel-wise variance ... done
>>>> >> Excluding voxels with constant value ... done
>>>> >>
>>>> >> Data size : 147 x 106223
>>>> >>
>>>> >> Starting PCA ... done
>>>> >> Start whitening using 49 dimensions ...
>>>> >> retaining 88.3302 percent of the variability
>>>> >> ... done
>>>> >>
>>>> >> Starting ICA estimation using symm
>>>> >>
>>>> >> Step no. 1 change : 0.422912
>>>> >> Step no. 2 change : 0.509312
>>>> >> Step no. 3 change : 0.458818
>>>> >> Step no. 4 change : 0.490924
>>>> >> .
>>>> >> .
>>>> >> .
>>>> >> Step no. 63 change : 5.50092e-05
>>>> >> Step no. 64 change : 5.21687e-05
>>>> >> Step no. 65 change : 5.06082e-05
>>>> >> Step no. 66 change : 4.94706e-05
>>>> >> Convergence after 66 steps
>>>> >>
>>>> >> Sorting IC maps
>>>> >>
>>>> >> Writing results to :
>>>> >> filtered_func_data.ica/melodic_IC
>>>> >> filtered_func_data.ica/melodic_Tmodes
>>>> >> filtered_func_data.ica/melodic_mix
>>>> >> filtered_func_data.ica/melodic_FTmix
>>>> >> filtered_func_data.ica/melodic_PPCA
>>>> >> filtered_func_data.ica/melodic_ICstats
>>>> >> filtered_func_data.ica/mask
>>>> >> ...done
>>>> >> Creating report index page ...done
>>>> >>
>>>> >>
>>>> >> Running Mixture Modelling on Z-transformed IC maps ...
>>>> >> IC map 1 ...
>>>> >> calculating mixture-model fit
>>>> >> saving probability map: filtered_func_data.ica/stats/probmap_1
>>>> >> saving mixture model fit: filtered_func_data.ica/stats/MMstats_1
>>>> >> re-scaling spatial maps ...
>>>> >> thresholding ...
>>>> >> alternative hypothesis test at p > 0.5
>>>> >> saving thresholded Z-stats image:
>>>> filtered_func_data.ica/stats/thresh_zstat1
>>>> >> creating report page ... done
>>>> >> .
>>>> >> .
>>>> >> .
>>>> >> IC map 49 ...
>>>> >> calculating mixture-model fit
>>>> >> saving probability map: filtered_func_data.ica/stats/probmap_49
>>>> >> saving mixture model fit: filtered_func_data.ica/stats/MMstats_49
>>>> >> re-scaling spatial maps ...
>>>> >> thresholding ...
>>>> >> alternative hypothesis test at p > 0.5
>>>> >> saving thresholded Z-stats image:
>>>> filtered_func_data.ica/stats/thresh_zstat49
>>>> >> creating report page ... done
>>>> >>
>>>> >> Ahmad
>>>> >>
>>>> >
>>>> >
>>>> >
>>>> ---------------------------------------------------------------------------
>>>> > Stephen M. Smith, Professor of Biomedical Engineering
>>>> > Associate Director, Oxford University FMRIB Centre
>>>> >
>>>> > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>> > +44 (0) 1865 222726 (fax 222717)
>>>> > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>> >
>>>> ---------------------------------------------------------------------------
>>>> >
>>>> > Stop the cultural destruction of Tibet
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>>
>>>
>>>
>>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 13:25:39 -0400
> From: Supreet kaur <[log in to unmask]>
> Subject: Re: Neonatal TBSS
>
> Hi Joseph,
>
> Thanks for your reply, it was helpful. So basically you applied FLIRT,
> FNIRT and applywarp to the subject FA images (on every other subject FA
> image)? I tried applying the FNIRT on the FA
> images, but unfortunately the results weren't good. I've been taking 22
> pre-term infants and 15 control term infant FA images.
> You have any suggestions to how many subject we can pick in a single
> analysis?
> You said you replaced three steps, did u apply the last fourth step of mean
> threshold of 0.2?
>
> I'll appreciate your feedback.
> Thanks,
> Supreet.
>
>
>
>
>
>
>
>
> On Wed, Jun 5, 2013 at 1:05 PM, Ackerman, JosephJr. <[log in to unmask]
>> wrote:
>
>> Hello Supreet.
>>
>>
>>
>> I also used TBSS on neonatal brains and found that fsl_reg (with the –FA
>> option) did a poor job since it assumes adult parameters. I had to rewrite
>> the tbss steps 1-3 in order to get more reliable registration for linear
>> and non-linear fits. I basically removed the fsl_reg part and inserted a
>> triple step of flirt, fnirt and applywarp (which is what fsl_reg
>> employees). I also built in an option to not use and atlas space at all
>> and stay in target space so as not to resample the data again. For the
>> global measures I was looking at I saw no real difference when not
>> transforming the data from native, to target or native, to target, to
>> atlas.
>>
>>
>>
>> The results seem to be working well.
>>
>>
>>
>> As well I did my alignments and transformations on the frame1 (the b0
>> volume(s)) from my subjects and then applied those matrix transformations
>> to the FA volumes. For my subjects the FA volumes were not the easiest to
>> align when using only them.
>>
>>
>>
>> Hope this helps in a little way. It can be done.
>>
>>
>>
>> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On
>> Behalf Of *Supreet kaur
>> *Sent:* Tuesday, June 04, 2013 11:03 AM
>> *To:* [log in to unmask]
>> *Subject:* [FSL] Neonatal TBSS
>>
>>
>>
>> Dear FSL experts,
>>
>> I am trying to analyze the TBSS in neonatal brains .However, the standard
>> space used for the non-linear registeration of FA maps, does not seem to
>> be working well:
>>
>> Is someone working with the neonatal brain images for the TBSS.
>>
>> I'd appreciate your response.
>>
>> Thanks in advance.
>>
>>
>>
>> Sincerely,
>>
>> Supreet
>>
>>
>>
>> ------------------------------
>>
>> The material in this message is private and may contain Protected
>> Healthcare Information (PHI). If you are not the intended recipient, be
>> advised that any unauthorized use, disclosure, copying or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited. If you have received this email in error, please immediately
>> notify the sender via telephone or return mail.
>>
>
>
>
> --
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 17:45:18 +0000
> From: "Ackerman, JosephJr." <[log in to unmask]>
> Subject: Re: Neonatal TBSS
>
> I did a threshold of .15 on the last step. In our data we found the noise floor to be about .12 so I felt comfortable with .15 being above the noise.
>
> I applied FLIRT,FNIRT and applywarp to the b0 volumes of my diffusion sets. The diffusion volumes were used to create the FA maps and thus the alignment between a subjects b0 volume and created FA is perfect. The FLIRT, FNIRT and APPLYwarp scripts have a much easier and accurate time aligning the b0 volumes (which are essentially anatomic T2W images). In step 2 I used one of my brains as a designated Target (-t) (I picked one of the best looking and nicely oriented, which for me was straight planar (XYZ, no tilt).
>
> So for every subject I had an FA and b0 volume. I rewrote the code to align the b0 and then take the transformation matrix (or affine) generated in that registration and applied it to that subjects FA volume.
>
> So for every patient you would align subject's b0 first to the target b0 and then to the atlas (which I changed to a neonatal atlas). Then I applied that transformation to the subjects FA. Do that for every subject and you have all the FA volumes in alignment and same space and ready to be merged.
>
> My neonates were all between 36-40 weeks but I had two group (control and injury) and was able to run 36 control against 71 injured.
>
> (It was not the easiest to recode, I admit (and I am not a pro coder).)
>
> Are you using FSL to generate your FA maps? I did it with in house software.
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Supreet kaur
> Sent: Wednesday, June 05, 2013 12:26 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Neonatal TBSS
>
> Hi Joseph,
> Thanks for your reply, it was helpful. So basically you applied FLIRT, FNIRT and applywarp to the subject FA images (on every other subject FA image)? I tried applying the FNIRT on the FA
> images, but unfortunately the results weren't good. I've been taking 22 pre-term infants and 15 control term infant FA images.
> You have any suggestions to how many subject we can pick in a single analysis?
> You said you replaced three steps, did u apply the last fourth step of mean threshold of 0.2?
>
> I'll appreciate your feedback.
> Thanks,
> Supreet.
>
>
>
>
>
>
> On Wed, Jun 5, 2013 at 1:05 PM, Ackerman, JosephJr. <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Hello Supreet.
>
> I also used TBSS on neonatal brains and found that fsl_reg (with the -FA option) did a poor job since it assumes adult parameters. I had to rewrite the tbss steps 1-3 in order to get more reliable registration for linear and non-linear fits. I basically removed the fsl_reg part and inserted a triple step of flirt, fnirt and applywarp (which is what fsl_reg employees). I also built in an option to not use and atlas space at all and stay in target space so as not to resample the data again. For the global measures I was looking at I saw no real difference when not transforming the data from native, to target or native, to target, to atlas.
>
> The results seem to be working well.
>
> As well I did my alignments and transformations on the frame1 (the b0 volume(s)) from my subjects and then applied those matrix transformations to the FA volumes. For my subjects the FA volumes were not the easiest to align when using only them.
>
> Hope this helps in a little way. It can be done.
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of Supreet kaur
> Sent: Tuesday, June 04, 2013 11:03 AM
> To: [log in to unmask]<mailto:[log in to unmask]>
> Subject: [FSL] Neonatal TBSS
>
> Dear FSL experts,
> I am trying to analyze the TBSS in neonatal brains .However, the standard space used for the non-linear registeration of FA maps, does not seem to be working well:
> Is someone working with the neonatal brain images for the TBSS.
> I'd appreciate your response.
> Thanks in advance.
>
> Sincerely,
>
> Supreet
>
>
> ________________________________
>
> The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
>
>
> --
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 14:02:06 -0400
> From: Supreet kaur <[log in to unmask]>
> Subject: Re: Neonatal TBSS
>
> Thanks Joseph,
>
> No I am using DTI Studio to generate my FA, b0, Trace map, and eigenvalue
> images. I agree that using FSL shell scripting code
> is not easy..But its one of the challenges we have in our lab.
> Thanks,
> Supreet
>
>
> On Wed, Jun 5, 2013 at 1:45 PM, Ackerman, JosephJr. <[log in to unmask]
>> wrote:
>
>> I did a threshold of .15 on the last step. In our data we found the
>> noise floor to be about .12 so I felt comfortable with .15 being above the
>> noise. ****
>>
>> ** **
>>
>> I applied FLIRT,FNIRT and applywarp to the b0 volumes of my diffusion
>> sets. The diffusion volumes were used to create the FA maps and thus the
>> alignment between a subjects b0 volume and created FA is perfect. The
>> FLIRT, FNIRT and APPLYwarp scripts have a much easier and accurate time
>> aligning the b0 volumes (which are essentially anatomic T2W images). In
>> step 2 I used one of my brains as a designated Target (-t) (I picked one of
>> the best looking and nicely oriented, which for me was straight planar
>> (XYZ, no tilt). ****
>>
>> ** **
>>
>> So for every subject I had an FA and b0 volume. I rewrote the code to
>> align the b0 and then take the transformation matrix (or affine) generated
>> in that registration and applied it to that subjects FA volume. ****
>>
>> ** **
>>
>> So for every patient you would align subject’s b0 first to the target b0
>> and then to the atlas (which I changed to a neonatal atlas). Then I
>> applied that transformation to the subjects FA. Do that for every subject
>> and you have all the FA volumes in alignment and same space and ready to be
>> merged.****
>>
>> ** **
>>
>> My neonates were all between 36-40 weeks but I had two group (control and
>> injury) and was able to run 36 control against 71 injured.****
>>
>> ** **
>>
>> (It was not the easiest to recode, I admit (and I am not a pro coder).)***
>> *
>>
>> ** **
>>
>> Are you using FSL to generate your FA maps? I did it with in house
>> software.****
>>
>> ** **
>>
>> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On
>> Behalf Of *Supreet kaur
>> *Sent:* Wednesday, June 05, 2013 12:26 PM
>> *To:* [log in to unmask]
>> *Subject:* Re: [FSL] Neonatal TBSS****
>>
>> ** **
>>
>> Hi Joseph,****
>>
>> Thanks for your reply, it was helpful. So basically you applied FLIRT,
>> FNIRT and applywarp to the subject FA images (on every other subject FA
>> image)? I tried applying the FNIRT on the FA****
>>
>> images, but unfortunately the results weren't good. I've been taking 22
>> pre-term infants and 15 control term infant FA images.****
>>
>> You have any suggestions to how many subject we can pick in a single
>> analysis? ****
>>
>> You said you replaced three steps, did u apply the last fourth step of
>> mean threshold of 0.2? ****
>>
>> ** **
>>
>> I'll appreciate your feedback.
>> Thanks,
>> Supreet.****
>>
>>
>>
>>
>>
>>
>> ****
>>
>> ** **
>>
>> On Wed, Jun 5, 2013 at 1:05 PM, Ackerman, JosephJr. <
>> [log in to unmask]> wrote:****
>>
>> Hello Supreet.****
>>
>> ****
>>
>> I also used TBSS on neonatal brains and found that fsl_reg (with the –FA
>> option) did a poor job since it assumes adult parameters. I had to rewrite
>> the tbss steps 1-3 in order to get more reliable registration for linear
>> and non-linear fits. I basically removed the fsl_reg part and inserted a
>> triple step of flirt, fnirt and applywarp (which is what fsl_reg
>> employees). I also built in an option to not use and atlas space at all
>> and stay in target space so as not to resample the data again. For the
>> global measures I was looking at I saw no real difference when not
>> transforming the data from native, to target or native, to target, to
>> atlas. ****
>>
>> ****
>>
>> The results seem to be working well. ****
>>
>> ****
>>
>> As well I did my alignments and transformations on the frame1 (the b0
>> volume(s)) from my subjects and then applied those matrix transformations
>> to the FA volumes. For my subjects the FA volumes were not the easiest to
>> align when using only them. ****
>>
>> ****
>>
>> Hope this helps in a little way. It can be done.****
>>
>> ****
>>
>> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On
>> Behalf Of *Supreet kaur
>> *Sent:* Tuesday, June 04, 2013 11:03 AM
>> *To:* [log in to unmask]
>> *Subject:* [FSL] Neonatal TBSS****
>>
>> ****
>>
>> Dear FSL experts,****
>>
>> I am trying to analyze the TBSS in neonatal brains .However, the standard
>> space used for the non-linear registeration of FA maps, does not seem to
>> be working well:****
>>
>> Is someone working with the neonatal brain images for the TBSS.****
>>
>> I'd appreciate your response.****
>>
>> Thanks in advance.
>> ****
>>
>> ****
>>
>> Sincerely,
>>
>> Supreet ****
>>
>> ****
>>
>> ** **
>> ------------------------------
>>
>>
>> The material in this message is private and may contain Protected
>> Healthcare Information (PHI). If you are not the intended recipient, be
>> advised that any unauthorized use, disclosure, copying or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited. If you have received this email in error, please immediately
>> notify the sender via telephone or return mail.****
>>
>>
>>
>>
>> -- ****
>>
>> Sincerely,
>>
>> Supreet kaur,****
>>
>> Biomedical research engineer,
>> Nationwide Childrens Hospital,
>> Columbus, OH
>> (614)355-3509****
>>
>
>
>
> --
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 21:27:25 +0100
> From: Saman Sarraf <[log in to unmask]>
> Subject: Re: Dual Regression, Image Exception : #22 :: ERROR, filenames can be basenames or not - RSVP
>
> Hey Steve,
>
> This is what I see in drA
> /Users/samansarraf/Downloads/FSL/fsl/bin/fslmaths /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4564/20090220_124047MWalzheimersJAN0910s011a1001_ADRS2mm.ica/reg_standard/filtered_func_data -Tstd -bin GROTAD/mask_00000 -odt char
> /Users/samansarraf/Downloads/FSL/fsl/bin/fslmaths /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4599/20090304_104451MWalzheimersJAN0910s011a1001_ADRS2mm.ica/reg_standard/filtered_func_data -Tstd -bin GROTAD/mask_00001 -odt char
> /Users/samansarraf/Downloads/FSL/fsl/bin/fslmaths /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4618/20090309_145615ALZHEIMERSSTUDY5MAR0s010a1001_ADRS2mm.ica/
> ... to the end
>
> I checked all drA.eXXXX.X, they are empty!
> I also checked all drA.oXXXX.X, all of them are empty!
> drB.e(o)XXXX. are empty too.
>
> This is drC:
>
> /Users/samansarraf/Downloads/FSL/fsl/bin/fsl_glm -i /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4564/20090220_124047MWalzheimersJAN0910s011a1001_ADRS2mm.ica/reg_standard/filtered_func_data -d /Users/samansarraf/Desktop/ADRS2mm.gica/groupmelodic.ica/melodic_IC -o GROTAD/dr_stage1_subject00000.txt --demean -m GROTAD/mask ; /Users/samansarraf/Downloads/FSL/fsl/bin/fsl_glm -i /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4564/20090220_124047MWalzheimersJAN0910s011a1001_ADRS2mm.ica/reg_standard/filtered_func_data -d GROTAD/dr_stage1_subject00000.txt -o GROTAD/dr_stage2_subject00000 --out_z=GROTAD/dr_stage2_subject00000_Z --demean -m GROTAD/mask --des_norm ; /Users/samansarraf/Downloads/FSL/fsl/bin/fslsplit GROTAD/dr_stage2_subject00000 GROTAD/dr_stage2_subject00000_ic
> /Users/samansarraf/Downloads/FSL/fsl/bin/fsl_glm -i /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4599/20090304_104451MWalzheimersJAN0910s011a1001_ADRS2mm.ica/reg_standard/filtered_func_data -d /Users/samansarraf/Desktop/ADRS2mm.gica/groupmelodic.ica/melodic_IC -o GROTAD/dr_stage1_subject00001.txt --demean -m GROTAD/mask ; /Users/samansarraf/Downloads/FSL/fsl/bin/fsl_glm -i /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4599/20090304_104451MWalzheimersJAN0910s011a1001_ADRS2mm.ica/reg_standard/filtered_func_data -d GROTAD/dr_stage1_subject00001.txt -o GROTAD/dr_stage2_subject00001 --out_z=GROTAD/dr_stage2_subject00001_Z --demean -m GROTAD/mask --des_norm ; /Users/samansarraf/Downloads/FSL/fsl/bin/fslsplit GROTAD/dr_stage2_subject00001 GROTAD/dr_stage2_subject00001_ic
> ... to the end
>
> And this is drC.eXXXX.X
>
> ols_dof: Error in determining the trace, resorting to basic calculation
> /bin/sh: line 1: 10307 Segmentation fault: 11 /Users/samansarraf/Downloads/FSL/fsl/bin/fsl_glm -i /Users/samansarraf/Desktop/Alzh_Nifti/AD_NIFTI/AD_data/4564/20090220_124047MWalzheimersJAN0910s011a1001_ADRS2mm.ica/reg_standard/filtered_func_data -d /Users/samansarraf/Desktop/ADRS2mm.gica/groupmelodic.ica/melodic_IC -o GROTAD/dr_stage1_subject00000.txt --demean -m GROTAD/mask
> Could not open matrix file GROTAD/dr_stage1_subject00000.txt
> ols_dof: Error in determining the trace, resorting to basic calculation
> Cannot open volume GROTAD/dr_stage2_subject00000 for reading!
>
> This issue is repeated in each drC.eXXXX.X!!!!!
> And drC.oXXXX.X s are empty.
>
> I appreciate if you can share your ideas with me.
>
> Best,
>
> Sam.
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 21:36:16 +0100
> From: Ella Hinton <[log in to unmask]>
> Subject: length of ISI?
>
> Hi all,
>
> I am preparing a simple food cue reactivity task for BOLD using an event related design. At the moment, the programme presents images from three conditions (50 in each) in a pseudo-random sequence, each image for 3 seconds followed by a fixation cross for a mean ISI of 1 second to provide the jitter. The sequence has been prepared such that all conditions precede and follow each other equally.
>
> But, after reading some messages on here and talking to others, should I have a longer mean ISI, or perhaps include null trials instead (rather than a jittered fixation cross after every image)? I would like to optimise the sequence to be able to detect and discriminate between the events in three conditions (contrasting each condition with the others).
>
> I would be grateful for advice regarding the optimal ISI in a design such as this.
> With thanks
> Ella
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 21:09:39 +0000
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: sienax with betted image...
>
> No - as it crucially relies on the skull to calculate a scaling factor.
> All the best,
> Mark
>
>
> On 5 Jun 2013, at 16:50, Gonzalo Rojas Costa <[log in to unmask]> wrote:
>
>> Hi:
>>
>> How can I use sienax with a betted image ?...
>>
>> Sincerely,
>>
>>
>>
>> --
>> Gonzalo Rojas Costa
>> Laboratory for Advanced Medical Image Processing
>> Department of Radiology
>> Clínica las Condes
>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>> Tel: 56-2-2105170
>> Cel: 56-9-97771785
>> www.clc.cl
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 21:11:37 +0000
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: cluster command question
>
> Hi,
>
> You should not use the pre-thresholded image as an input (thresh_zstat1).
> Use a raw zstat image from the stats folder instead (zstat1).
>
> All the best,
> Mark
>
>
>
> On 5 Jun 2013, at 17:17, Mark <[log in to unmask]> wrote:
>
>> Hi,
>>
>> I've searched the archive still can't figure out the problem I encountered. I know that by default only 6 local maxima (LM) are reported per cluster. In one of my contrast (thresholded at z=2.0), I identified one big cluster, and Firefox reported 6 LMs:
>>
>> Cluster Index Z x y z
>> 1 3.59 4 -64 48
>> 1 2.69 10 -52 40
>> 1 2.63 4 -46 46
>> 1 2.54 10 -70 44
>> 1 2.52 0 -76 38
>> 1 2.51 18 -74 42
>>
>> I's like to get more LMs within this cluster. So I performed "cluster -i cope.feat/thresh_zstat1.nii.gz -t 2.0 -n 10 --mm" and the results were:
>>
>> Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm)
>> 1 896 3.59 4 -64 48 5.76 -64 43.7
>>
>> Why only one LM was yielded?
>>
>> Thanks in advance.
>>
>> Mark
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 21:32:07 +0000
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: Registration quality
>
> Hi,
>
> When I ran this registration with the default recommendations (BBR for example_func to highres, and 12 DOF + nonlinear for the highres to standard) I got very good registrations, which were a _lot_ better than the ones you sent. Is there any reason you were not using the defaults?
>
> All the best,
> Mark
>
>
>
> On 4 Jun 2013, at 14:45, Maren Strenziok <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Hi Mark,
>
> I uploaded those two images.
>
> Thanks, Maren
>
>
> On Mon, Jun 3, 2013 at 6:26 PM, Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Hi,
>
> I'm afraid these files are not useful on their own.
> I also need to see the example_func and highres images.
>
> All the best,
> Mark
>
>
> On 3 Jun 2013, at 14:56, Maren Strenziok <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Hi Mark,
>
> the BET result looks fine. I just uploaded two nifti files, example_func2standard and example_func2highres. I put my first name in the name of the files so that you can easily find them on your server. Please let me know if you needed any additional files.
>
> Best regards, Maren
>
>
> On Thu, May 30, 2013 at 4:18 AM, Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Hi,
>
> That does look bad to me. Have you checked that the brain extractions are OK?
> It is hard to diagnose anything without more information though. Can you upload the relevant nifti images to this site:
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
> then I'll have a look at them and hopefully figure out a way to improve the results.
>
> All the best,
> Mark
>
>
> On 28 May 2013, at 15:39, Maren Strenziok <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> I have trouble to judge the quality of a registration result. I registered an fMRI scan (acquired with 3x3x3 resolution, large field of view) to 1mm MNI standard space via a high resolution mprage (roughly 1x1x1 resolution). I used normal search, 12 DoF for the mprage and for the standard brain. I checked non-linear for the registration to standard space. The registration of the functional data to the standard brain (and also to the mprage) don't look good (see attached image) compared to what I have seen before using another imaging program. Am I too picky or is there a way to get better results? Could the poor quality be related to an error message that I get when I load in the data? It says: Warning - have auto-set BET preprocessing option and/or registration DoF on the basis of image fields-of-view; check settings.
>
> Maren
> <Doc1.docx>
>
>
>
>
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 21:35:06 +0000
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: fslmeants error
>
> Hi,
>
> We've not got any specific tools for speeding this up, as it isn't something we've really come across much. So you could either remap the labels with some other program (e.g. matlab) or just put up with the wait.
>
> All the best,
> Mark
>
>
>
> On 3 Jun 2013, at 11:26, Ricardo Magalhães <[log in to unmask]> wrote:
>
>> so, using --label=/roifile fixed it, but now i would like to try something to optimize it. I am using a freesurfer aparc2009+aseg segmentation as my set of ROIs, and it has 192 regions, ranging from 2 to 12175. fslmeants searches every value in between meaning it will take about 3 hours to run and produce alot of useless 0s. I would like to know if there is anyway way i can restrict the values being searched to just those i know are on the image. Or If there is any tool i can use to replace the values of the image, replacing 2 with 1, 4 with 2 (...) 12175 with 192.
>> Thanks for any help, Ricardo
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 21:41:00 +0000
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: visualizing results
>
> Hi,
>
> This is not a well-formed image as the number of voxels are consistent with a 3mm image (dim1-dim3 in the range 60-72) but the voxel sizes are wrong (pixdim1-pixdim3=1.0). The easiest way to resample images onto the melodic standard-space output is to do:
> flirt -in $FSLDIR/data/standard/MNI152_T1_1mm -ref existing_melodic_image_3mm -usesqform -applyxfm -out mni_3mm
>
> This uses an existing melodic result (existing_melodic_image_3mm) that is already in the 3mm standard space, and then resamples the standard MNI image to make sure that the mm coordinates align (this is what the -usesqform option does). Other commands can also achieve the same result, but sometimes it can be more difficult because it might be off 1 in the number of voxels (e.g. 61 vs 60) and this is a problem for FSLView.
>
> All the best,
> Mark
>
>
>
> On 4 Jun 2013, at 21:58, Jacobs H (NP) <[log in to unmask]> wrote:
>
>> Hi FSL developers,
>>
>> I wanted to check my results from my resting state analyses in fslview.
>> In melodic I chose a resampling resolution of 3mm.
>> So, I thought I would need to check my dual regression on a 3mm isotropic standard brain of FSL? Therefore, I used mri_convert to resample it in 3mm.
>> However, my results do not fit on the standard MNI152_T1 1mm/2mm/3mm?
>> I checked my output file with fslhd and I copied the result below this email.
>> I was able to check the results on the bg_image.nii.gz. So, that was not a problem, but the atlas did not work properly (stating that the parietal lobe is the frontal lobe)?
>>
>> Any help?
>>
>> Thanks
>> Heidi
>>
>> sizeof_hdr 348
>> data_type FLOAT32
>> dim0 3
>> dim1 60
>> dim2 72
>> dim3 60
>> dim4 1
>> dim5 1
>> dim6 1
>> dim7 1
>> vox_units mm
>> time_units s
>> datatype 16
>> nbyper 4
>> bitpix 32
>> pixdim0 0.0000000000
>> pixdim1 1.0000000000
>> pixdim2 1.0000000000
>> pixdim3 1.0000000000
>> pixdim4 1.0000000000
>> pixdim5 0.0000000000
>> pixdim6 0.0000000000
>> pixdim7 0.0000000000
>> vox_offset 352
>> cal_max 0.0000
>> cal_min 0.0000
>> scl_slope 1.000000
>> scl_inter 0.000000
>> phase_dim 0
>> freq_dim 0
>> slice_dim 0
>> slice_name Unknown
>> slice_code 0
>> slice_start 0
>> slice_end 0
>> slice_duration 0.000000
>> time_offset 0.000000
>> intent Unknown
>> intent_code 0
>> intent_name
>> intent_p1 0.000000
>> intent_p2 0.000000
>> intent_p3 0.000000
>> qform_name Unknown
>> qform_code 0
>> qto_xyz:1 1.000000 0.000000 0.000000 0.000000
>> qto_xyz:2 0.000000 1.000000 0.000000 0.000000
>> qto_xyz:3 0.000000 0.000000 1.000000 0.000000
>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>> qform_xorient Left-to-Right
>> qform_yorient Posterior-to-Anterior
>> qform_zorient Inferior-to-Superior
>> sform_name Unknown
>> sform_code 0
>> sto_xyz:1 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:2 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:3 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:4 0.000000 0.000000 0.000000 0.000000
>> sform_xorient Unknown
>> sform_yorient Unknown
>> sform_zorient Unknown
>> file_type NIFTI-1+
>> file_code 1
>> descrip FSL5.0
>> aux_file
>>
>>
>>
>> ================================================
>> Dr. Heidi Jacobs
>> Postdoc researcher
>> Faculty of Health, Medicine and Life Sciences
>> School for Mental Health and Neurosciences
>> Division Cognitive Neuropsychiatry and Clinical Neurosciences
>> Alzheimer Center Limburg
>> [log in to unmask]
>> www.maastrichtuniversity.nl
>> www.heidijacobs.nl
>>
>> Dr. Tanslaan 12, 6229 ET Maastricht
>> P.O. Box 616, 6200 MD Maastricht, The Netherlands
>> T +31 43 38 84 090 F +31 43 38 84 092
>> ================================================
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 22:49:32 +0100
> From: Joyce Yu Guo <[log in to unmask]>
> Subject: 2X2 ANOVA interaction
>
> Dear fsler,
>
> I have questions about my 2x2 ANOVA interaction. I have two main effects: diagnosis group (patient and control ) and age (young and old). There are 2 subjects in each subgroup which makes 8 subjects in total. The design matrix of ANOVA looks like following
>
> age diagnosis interaction mean
> 1 1 1 1
> 1 1 1 1
> 1 -1 -1 1
> 1 -1 -1 1
> -1 1 -1 1
> -1 1 -1 1
> -1 -1 1 1
> -1 -1 1 1
>
> contrast:
>
> F1 F2 F3
> C1 1 0 0 0 X
> C2 0 1 0 0 X
> C3 0 0 1 0 X
> C4 -1 0 0 0
> C5 0 -1 0 0
> C6 0 0 -1 0
>
> The significant brain activities was found on all three F contrasts which means significant brain activity between age, diagnosis and age by diagnosis interaction. As interaction between two main effect showed significant in my model, in normal statistic test, I then need to check post hoc to explore one main effect according to each level of another main effect. I would like to know how can I achieve this in fsl?
>
> When I checked the t-test results: C1-C6 there are only C4 showed significant brain activities. Should not C3 and C6 be significant?
>
> bw,
> Joyce
>
> ------------------------------
>
> Date: Thu, 6 Jun 2013 00:04:45 +0200
> From: "Christian F. Beckmann" <[log in to unmask]>
> Subject: Re: Resting state fMRI using MELODIC
>
> Hi
>
> The address is https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
>
> hth
> Christian
>
> On 5 Jun 2013, at 19:22, Ahmad Omar <[log in to unmask]> wrote:
>
>> Hi Steve,
>>
>> Would you please send me the web page address to upload a data set for you to look at?
>>
>> Thanks for your assistance.
>> Ahmad
>>
>> Ahmad Omar
>>
>>
>>
>> On Mon, Jun 3, 2013 at 5:44 PM, Ahmad Omar <[log in to unmask]> wrote:
>> Hi Christian,
>>
>> Would you please send me the web page address to upload a data set for you to look at?
>>
>> Thanks for your assistance.
>> Ahmad
>>
>> Ahmad Omar
>>
>>
>>
>> On Fri, May 31, 2013 at 9:10 PM, Ahmad Omar <[log in to unmask]> wrote:
>> Hi Christian,
>>
>> The runs we have been doing have been on a single subject. You suspect that the data set is bad, right? I will try to upload it from the center.
>>
>> Thanks for your help.
>> Ahmad
>>
>> Ahmad Omar
>>
>>
>>
>> On Fri, May 31, 2013 at 8:56 AM, Christian F. Beckmann <[log in to unmask]> wrote:
>> Hi,
>>
>> I suggest running single-subject ICAs first, just to see if the data quality per se is OK or if you happen to have strange artefacts in your data. If you cannot make this work then feel free to upload a single data set so we can see what's going on...
>>
>> hth
>> Christian
>>
>>
>>
>> On 31 May 2013, at 11:53, Ahmad Omar <[log in to unmask]> wrote:
>>
>> > Hi Steve,
>> >
>> > Thank you for your reply. Unfortunately, we are only getting what in some places are randomly scattered activations in the midbrain or concentrated activations in the frontal and orbito-frontal regions where there is already some epi-related distortions so not be relied upon . I was meaning to ask this follow-up question. Shouldn't I turn off temporal high pass filtering as I am interested in the ultra-low frequency BOLD
>> > signals? I tried a run doing that and the activation areas changed a bit to being around the ventricles and in the putamen which also looked strange to us.
>> >
>> > We very much appreciate your help on this.
>> >
>> > Ahmad
>> >
>> > Ahmad Omar
>> >
>> >
>> >
>> > On Thu, May 30, 2013 at 1:00 AM, Stephen Smith <[log in to unmask]> wrote:
>> > Hi - there's nothing in this description or the log that jumps out at me - did you find *some* RSNs that you recognised?
>> > Steve.
>> >
>> > On 29 May 2013, at 16:31, Ahmad Omar <[log in to unmask]> wrote:
>> >
>> >>
>> >> Re-send. Thanks.
>> >>
>> >>
>> >> Ahmad Omar
>> >>
>> >>
>> >>
>> >> ---------- Forwarded message ----------
>> >> From: Ahmad Omar <[log in to unmask]>
>> >> Date: Mon, May 27, 2013 at 4:53 PM
>> >> Subject: Resting state fMRI using MELODIC
>> >> To: FSL Mailing List <[log in to unmask]>
>> >>
>> >>
>> >> Hello All,
>> >>
>> >> I am trying to apply MELODIC (ver. 3.13, FSL ver 5.0.4 on a virtual machine) to some resting-state fMRI data we are acquiring here at the radiology center. The scanner is a 3T Siemens Skyra. The sequence is the standard ep2d sequence acquiring 150 time points with TR = 2.57 sec, TE = 36 msec, flip angle = 75 deg, distance factor = 20, PAT = 2, Fat Sat. on, phase partial Fourier off, bandwidth = 1698 Hz/Px and 1.7mm x 1.7 mm x 5 mm (in the z-axis direction) resolution with interleaved slice acquisition. Motion correction and temporal high pass filtering were enabled in the scanner sequence. When I view and loop through the raw data in FSL View, it seems fine. No excessive translations or head rotation and no severe intensity variations. In MELODIC I set the following settings: Delete Volumes = 3, High pass filter cutoff (s) = 100, Motion Correction : MCFLIRT, Slice timing correction: Interleaved, spatial smoothing FWHM (mm) = 5, Temporal filtering: Highpass, Threshold IC maps left at 0.5 and output the full stats folder was enabled. We were trying to reproduce the work done by Tang, L et al. in the paper "Thalamic Resting-State Functional Networks: Disruption in Patients with Mild Traumatic Brain Injury". MELODIC finishes processing fine but we don't know why we are not seeing any meaningful activations in say the Default Mode Network areas let alone activations in the thalamus. I have included below a part of the log.txt file in the filtered_func_data.ica folder.
>> >>
>> >> Thanks and your help is much appreciated.
>> >>
>> >> Melodic Version 3.13
>> >>
>> >> /usr/local/fsl/bin/melodic -i filtered_func_data -o filtered_func_data.ica -v --nobet --bgthreshold=3 --tr=2.5699999332 --report --guireport=../../report.html -d 0 --mmthresh=0.5 --Ostats
>> >> ---------------------------------------------
>> >>
>> >> Melodic results will be in filtered_func_data.ica
>> >>
>> >> Create mask ... done
>> >> Reading data file filtered_func_data ... done
>> >> Estimating data smoothness ... done
>> >> Removing mean image ... done
>> >> Normalising by voxel-wise variance ... done
>> >> Excluding voxels with constant value ... done
>> >>
>> >> Data size : 147 x 106223
>> >>
>> >> Starting PCA ... done
>> >> Start whitening using 49 dimensions ...
>> >> retaining 88.3302 percent of the variability
>> >> ... done
>> >>
>> >> Starting ICA estimation using symm
>> >>
>> >> Step no. 1 change : 0.422912
>> >> Step no. 2 change : 0.509312
>> >> Step no. 3 change : 0.458818
>> >> Step no. 4 change : 0.490924
>> >> .
>> >> .
>> >> .
>> >> Step no. 63 change : 5.50092e-05
>> >> Step no. 64 change : 5.21687e-05
>> >> Step no. 65 change : 5.06082e-05
>> >> Step no. 66 change : 4.94706e-05
>> >> Convergence after 66 steps
>> >>
>> >> Sorting IC maps
>> >>
>> >> Writing results to :
>> >> filtered_func_data.ica/melodic_IC
>> >> filtered_func_data.ica/melodic_Tmodes
>> >> filtered_func_data.ica/melodic_mix
>> >> filtered_func_data.ica/melodic_FTmix
>> >> filtered_func_data.ica/melodic_PPCA
>> >> filtered_func_data.ica/melodic_ICstats
>> >> filtered_func_data.ica/mask
>> >> ...done
>> >> Creating report index page ...done
>> >>
>> >>
>> >> Running Mixture Modelling on Z-transformed IC maps ...
>> >> IC map 1 ...
>> >> calculating mixture-model fit
>> >> saving probability map: filtered_func_data.ica/stats/probmap_1
>> >> saving mixture model fit: filtered_func_data.ica/stats/MMstats_1
>> >> re-scaling spatial maps ...
>> >> thresholding ...
>> >> alternative hypothesis test at p > 0.5
>> >> saving thresholded Z-stats image: filtered_func_data.ica/stats/thresh_zstat1
>> >> creating report page ... done
>> >> .
>> >> .
>> >> .
>> >> IC map 49 ...
>> >> calculating mixture-model fit
>> >> saving probability map: filtered_func_data.ica/stats/probmap_49
>> >> saving mixture model fit: filtered_func_data.ica/stats/MMstats_49
>> >> re-scaling spatial maps ...
>> >> thresholding ...
>> >> alternative hypothesis test at p > 0.5
>> >> saving thresholded Z-stats image: filtered_func_data.ica/stats/thresh_zstat49
>> >> creating report page ... done
>> >>
>> >> Ahmad
>> >>
>> >
>> >
>> > ---------------------------------------------------------------------------
>> > Stephen M. Smith, Professor of Biomedical Engineering
>> > Associate Director, Oxford University FMRIB Centre
>> >
>> > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> > +44 (0) 1865 222726 (fax 222717)
>> > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> > ---------------------------------------------------------------------------
>> >
>> > Stop the cultural destruction of Tibet
>> >
>> >
>> >
>> >
>> >
>>
>>
>>
>
> ------------------------------
>
> Date: Thu, 6 Jun 2013 00:16:49 +0200
> From: "Christian F. Beckmann" <[log in to unmask]>
> Subject: Re: MELODIC output report, Powerspectrum scaling
>
> Hi
>
> Just like in matlab it can happen that the default width of the plot (png file) will create x-tickmarks at e.g. 0 and 25 for a power spectral plot of length 30. In melodic a vertical line should indicate what point the labels refer to.
>
> hth
> Christian
>
>
>
>
> On 3 Jun 2013, at 22:22, Joel Bruss <[log in to unmask]> wrote:
>
>> Hello!
>>
>> I have a question about the output report from MELODIC. I'm looking at all of the IC outputs and the relevant Powerspectrum, e.g. f1.txt. If I were to use fsl_tsplot, I get, essentially, the same plot that you would see with the associated html file (IC_1.html). However, the x-axis scaling is different. I have, in my files, 60 timepoints but the MELODIC report has the x-axis labeled from 0-25. How is this file (f1.png) created (what is the command-line) and what is the reason that the x-axis is rescaled? Thanks for any and all responses.
>>
>> -Joel
>
> ------------------------------
>
> Date: Wed, 5 Jun 2013 23:16:49 +0100
> From: "Anderson M. Winkler" <[log in to unmask]>
> Subject: Re: design.mat & design.com in randomise
>
> Hi Elena,
>
> I am running a rsfMRI analysis (3 different groups) and I have some
>> questions about the randomise tool. Do I have to use the
>> exchangeability-block (design.grp) file?
>>
>
> No, not necessary here.
>
> I created the design and contrast matrix but I am also confused about
>> covariates and demeaning.I have 3EV's (one per group) and 2EV's (age &
>> gender). I demeaned the age and gender regressors. Is it correct?
>>
>
> Looks fine to me. The sex for one of the subjects is marked as
> -3.500000e-01, instead of -3.400000e-01 as the others, but this is so small
> that I doubt it will make any difference.
>
> All the best,
>
> Anderson
>
> ------------------------------
>
> End of FSL Digest - 4 Jun 2013 to 5 Jun 2013 (#2013-173)
> ********************************************************
|
