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Am 10.07.2015 um 01:00 schrieb FSL automatic digest system:
> There are 20 messages totaling 2441 lines in this issue.
>
> Topics of the day:
>
> 1. FSL installation question (3)
> 2. tbss_3_postreg for rodent data
> 3. FSLnets
> 4. PhD position Neuroimaging/Physics/Biomedical Engineering in Amsterdam
> 5. rfmri functional connectivity (2)
> 6. PALM - MANOVA/MANCOVA option
> 7. topup necessary? (8)
> 8. Too much activation
> 9. Feat Z Max values
> 10. FEAT second level analysis with standard space from ants
>
> ----------------------------------------------------------------------
>
> Date: Wed, 8 Jul 2015 17:46:47 -0700
> From: Siddharth Srivastava <[log in to unmask]>
> Subject: FSL installation question
>
> Hi All,
> I am trying to install FSL on a Ubuntu machine (trusty thar), and
> following
> instructions from the fsl.fmrib.ox.ac.uk fsldownloads page. I am, however,
> having a harrowing time understanding the whole process for Ubuntu users.
> What I have done do far:
> - selected the Debian/Ubuntu section, which led me to the neurodebian page
> for fsl.
> - as instructed, I used apt-get fsl-complete
> - the installation finished without errors
> Seemed simple, but when I set out to find where fsl was installed, I saw
> both
> fsl4.1* and fsl5.0* in /usr/bin/, also there was a /usr/share/fsl with 4.0
> and 5.0
> directories, and some links to /lib/fsl and /etc/ too.
>
> So, my questions are:
> - where is fsl installed after apt-get install
> - what is the best way to process after this? or is there another way?
> I can obviously try building from the source, but would rather avoid that...
>
> Thanks,
> Sid.
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 02:21:09 +0100
> From: Subscribe FSL Patrick McCunn <[log in to unmask]>
> Subject: tbss_3_postreg for rodent data
>
> Hi all
>
> I have a quick question. I've been working on analyzing rodent data with tbss. I've finally managed to run the entire process with a few modifications. My question though is during the 3rd step (tbss_3_postreg). While my data appears alright by the end of it the orientation is a little strange (i.e. tilted on odd axis) and I believe that is due to warping to MNI152 space. Looking at the script it appears that during the registration step (even when using -S) the FMRIB58_FA_1mm template is used as a reference when transforming to MNI152 space. So i have a couple questions here.
> Should i adjust my analysis to avoid transforming all my data to MNI152 space?
> If not, can I warp the rodent data to MNI space without using a human reference template?
>
> I hope this makes sense and I'm not way off track here.
>
> Patrick
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 05:53:46 +0200
> From: Michael Hanke <[log in to unmask]>
> Subject: Re: FSL installation question
>
> Hi,
>
> you choose which FSL version you want to use by sourcing the right config
> file. You find them in /etc/fsl/...
>
> Take a look at the manpage for more info.
>
> man fsl
>
> Cheers,
>
> Michael
> On Jul 9, 2015 02:46, "Siddharth Srivastava" <[log in to unmask]> wrote:
>
>> Hi All,
>> I am trying to install FSL on a Ubuntu machine (trusty thar), and
>> following
>> instructions from the fsl.fmrib.ox.ac.uk fsldownloads page. I am, however,
>> having a harrowing time understanding the whole process for Ubuntu users.
>> What I have done do far:
>> - selected the Debian/Ubuntu section, which led me to the neurodebian page
>> for fsl.
>> - as instructed, I used apt-get fsl-complete
>> - the installation finished without errors
>> Seemed simple, but when I set out to find where fsl was installed, I saw
>> both
>> fsl4.1* and fsl5.0* in /usr/bin/, also there was a /usr/share/fsl with 4.0
>> and 5.0
>> directories, and some links to /lib/fsl and /etc/ too.
>>
>> So, my questions are:
>> - where is fsl installed after apt-get install
>> - what is the best way to process after this? or is there another way?
>> I can obviously try building from the source, but would rather avoid
>> that...
>>
>> Thanks,
>> Sid.
>>
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 09:10:46 +0100
> From: paul mccarthy <[log in to unmask]>
> Subject: Re: FSLnets
>
> Hi Christophe,
>
> This is a known problem, and is occurring because the version of randomise
> that is shipped with FSL 5.0.8 does not produce uncorrected p value images
> by default, wherease FSLNets assumes that it does.
>
> You can overcome this error byby editing line 38 in nets_glm.m - add
> '--uncorrp' as a flag to the randomise call.
>
> Cheers,
>
> Paul
>
> On 8 July 2015 at 18:11, HABAS Christophe <[log in to unmask]> wrote:
>
>>
>> ------------------------------
>>
>> Hello,
>>
>> Unfortunately, another problem occured (just after the correct computation
>> of clustering):
>>
>> Critical Value for:
>> /tmp/tp2dc87715_94b8_4cda_af6e_da982ae12215_vox_corrp_tstat1 is: 4.73351
>> Finished, exiting.
>> Error using call_fsl (line 36)
>> FSL call (/bin/sh -c '. /usr/local/fsl/etc/fslconf/fsl.sh;
>> FSLOUTPUTTYPE=NIFTI_PAIR; export FSLOUTPUTTYPE;
>> $FSLDIR/bin/fslmaths
>> /tmp/tp2dc87715_94b8_4cda_af6e_da982ae12215_vox_p_tstat1
>> /tmp/tp4eab7ef7_a3c8_4029_b1ad_9f7ad3242be9')
>> failed, Cannot open volume
>> /tmp/tp2dc87715_94b8_4cda_af6e_da982ae12215_vox_p_tstat1 for reading!
>>
>>
>> Error in read_avw (line 24)
>> [status,output]=call_fsl(command);
>>
>> Error in nets_glm (line 51)
>> p_uncorrected(i,:)= read_avw(sprintf('%s_vox_p_tstat%d',fname,i));
>>
>> Error in nets_examples (line 68)
>> [p_uncorrected,p_corrected]=nets_glm(netmats1,'design.mat','design.con',1);
>> % returns matrices of 1-p
>>
>>
>>
>> Best,
>> Christophe
>> ------------------------------
>> *De :* HABAS Christophe
>> *Envoyé :* mercredi 8 juillet 2015 18:58
>> *À :* paul mccarthy
>> *Objet :* RE: [FSL] FSLnets
>>
>> Hello,
>>
>> Ok
>>
>> many thanks
>>
>> Best regards
>>
>> Christophe
>> ------------------------------
>> *De :* [log in to unmask] <[log in to unmask]> de la part de
>> paul mccarthy <[log in to unmask]>
>> *Envoyé :* mercredi 8 juillet 2015 18:52
>> *À :* HABAS Christophe
>> *Objet :* Re: [FSL] FSLnets
>>
>> Hi Christophe,
>>
>> Ok, all you need to do then is fix that path in nets_example.m :
>>
>> group_maps='/home/habas/Bureau ........
>>
>> Cheers,
>>
>> Paul
>>
>> On 8 July 2015 at 17:49, HABAS Christophe <[log in to unmask]> wrote:
>>
>>> Dear Paul,
>>>
>>> Thank you: you are right I wrote" bureau"instead of "Bureau" in the
>>> path!!!!
>>>
>>> Best regards,
>>> Christophe
>>>
>>> ------------------------------
>>> *De :* [log in to unmask] <[log in to unmask]> de la part de
>>> paul mccarthy <[log in to unmask]>
>>> *Envoyé :* mercredi 8 juillet 2015 18:43
>>>
>>> *À :* HABAS Christophe
>>> *Objet :* Re: [FSL] FSLnets
>>>
>>> Hi Christohphe,
>>>
>>> This is your problem - it looks like the melodic_IC.sum directory is
>>> located in the wrong place. I have two questions:
>>>
>>> 1. What directory did you originally run nets_examples in ?
>>>
>>> 2. From your existing melodic_IC.sum directory, could you please run
>>> the command:
>>>
>>> pwd
>>>
>>> Cheers,
>>>
>>> Paul
>>>
>>> On 8 July 2015 at 17:35, HABAS Christophe <[log in to unmask]> wrote:
>>>
>>>> Again sorry!
>>>>
>>>> [habas@HABAS ~]$ ls
>>>> ~/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum/
>>>> ls: impossible d'accéder à (= impoosible to access to")
>>>> /home/habas/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum/:
>>>> Aucun fichier ou dossier de ce type (=no files)
>>>> [habas@HABAS ~]$
>>>>
>>>> Beest,
>>>> Christophe
>>>>
>>>> ------------------------------
>>>> *De :* [log in to unmask] <[log in to unmask]> de la part
>>>> de paul mccarthy <[log in to unmask]>
>>>> *Envoyé :* mercredi 8 juillet 2015 18:22
>>>>
>>>> *À :* HABAS Christophe
>>>> *Objet :* Re: [FSL] FSLnets
>>>>
>>>> Hi Christophe,
>>>>
>>>> Could you please run this command exactly as I have specified it:
>>>>
>>>> ls ~/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum/
>>>>
>>>> Cheers,
>>>>
>>>> Paul
>>>>
>>>>
>>>> On 8 July 2015 at 17:21, HABAS Christophe <[log in to unmask]> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>>
>>>>> Sorry!
>>>>> [habas@HABAS melodic_IC.sum]$ ls
>>>>> 0000.png 0007.png 0014.png 0021.png 0028.png 0035.png 0042.png
>>>>> 0049.png
>>>>> 0001.png 0008.png 0015.png 0022.png 0029.png 0036.png 0043.png
>>>>> 0050.png
>>>>> 0002.png 0009.png 0016.png 0023.png 0030.png 0037.png 0044.png
>>>>> 0003.png 0010.png 0017.png 0024.png 0031.png 0038.png 0045.png
>>>>> 0004.png 0011.png 0018.png 0025.png 0032.png 0039.png 0046.png
>>>>> 0005.png 0012.png 0019.png 0026.png 0033.png 0040.png 0047.png
>>>>> 0006.png 0013.png 0020.png 0027.png 0034.png 0041.png 0048.png
>>>>>
>>>>> Best,
>>>>> Christophe
>>>>> ------------------------------
>>>>> *De :* [log in to unmask] <[log in to unmask]> de la part
>>>>> de paul mccarthy <[log in to unmask]>
>>>>> *Envoyé :* mercredi 8 juillet 2015 18:13
>>>>>
>>>>> *À :* HABAS Christophe
>>>>> *Objet :* Re: [FSL] FSLnets
>>>>>
>>>>> Hi Christophe,
>>>>>
>>>>> I am specifically asking for the output of this command - run it in a
>>>>> terminal, and send me the full output:
>>>>>
>>>>> ls ~/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum/
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Paul
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 8 July 2015 at 17:12, HABAS Christophe <[log in to unmask]> wrote:
>>>>>
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>>
>>>>>> Here is one of the 50 png images contained in melodic_IC.sum;
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Christophe
>>>>>> ------------------------------
>>>>>> *De :* [log in to unmask] <[log in to unmask]> de la part
>>>>>> de paul mccarthy <[log in to unmask]>
>>>>>> *Envoyé :* mercredi 8 juillet 2015 18:08
>>>>>> *À :* HABAS Christophe
>>>>>> *Objet :* Re: [FSL] FSLnets
>>>>>>
>>>>>> Hi Christohpe,
>>>>>>
>>>>>> Whether or not you get figure 1 is unrelated to this problem. Could
>>>>>> you please send me the output of this command:
>>>>>>
>>>>>> ls ~/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum/
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Paul
>>>>>>
>>>>>> On 8 July 2015 at 17:00, HABAS Christophe <[log in to unmask]> wrote:
>>>>>>
>>>>>>> Yes they are.
>>>>>>>
>>>>>>> Moreover, the first step of the script runs correctly as I get the
>>>>>>> figure 1.
>>>>>>>
>>>>>>> Thanks;
>>>>>>>
>>>>>>> Best,
>>>>>>> Christophe
>>>>>>> ------------------------------
>>>>>>> *De :* FSL - FMRIB's Software Library <[log in to unmask]> de la
>>>>>>> part de paul mccarthy <[log in to unmask]>
>>>>>>> *Envoyé :* mercredi 8 juillet 2015 17:30
>>>>>>> *À :* [log in to unmask]
>>>>>>> *Objet :* Re: [FSL] FSLnets
>>>>>>>
>>>>>>> Hi Christophe,
>>>>>>>
>>>>>>> Could you please confirm that the PNG images are in the correct
>>>>>>> location? Send the outpurt of
>>>>>>>
>>>>>>> ls ~/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum/
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Paul
>>>>>>>
>>>>>>> On 8 July 2015 at 11:12, Christophe Habas <[log in to unmask]>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I always get the same message:
>>>>>>>>
>>>>>>>>>> nets_examples
>>>>>>>>
>>>>>>>> /home/habas/Bureau/UMBRELLA/RP_late_blind.gica
>>>>>>>>
>>>>>>>>
>>>>>>>> Cannot open
>>>>>>>> /home/habas/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum/0002.png
>>>>>>>> for reading
>>>>>>>> /usr/local/fsl/bin/slices_summary: line 201: 12283 Segmentation
>>>>>>>> fault (core dumped) $thestring
>>>>>>>> slices_summary
>>>>>>>> /home/habas/bureau/UMBRELLA/RP_late_blind.gica/groupica.ica/melodic_IC.sum
>>>>>>>> /tmp/tpa9a03983_77b8_4dde_a8ef_bc6a5369931f.png 2 5 6 7 9 10 12
>>>>>>>> 13 14 15 16 17 19 21 22 24 27: Segmentation fault
>>>>>>>> Error using imread (line 350)
>>>>>>>> File "/tmp/tpa9a03983_77b8_4dde_a8ef_bc6a5369931f.png" does not
>>>>>>>> exist.
>>>>>>>>
>>>>>>>> Error in nets_nodepics (line 16)
>>>>>>>> pic=imread(sprintf('%s.png',grot));
>>>>>>>>
>>>>>>>> Error in nets_examples (line 37)
>>>>>>>> nets_nodepics(ts,group_maps); % quick views of the good
>>>>>>>> and bad components
>>>>>>>>
>>>>>>>>
>>>>>>>> I checked the paths which are correct and the .png images have been
>>>>>>>> correctly generated!
>>>>>>>>
>>>>>>>> I am lost.
>>>>>>>>
>>>>>>>> Thank you for your help.
>>>>>>>>
>>>>>>>> Best regards
>>>>>>>> Christophe
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 09:51:00 +0100
> From: Guido van Wingen <[log in to unmask]>
> Subject: PhD position Neuroimaging/Physics/Biomedical Engineering in Amsterdam
>
> Dear all,
>
> We are looking for a PhD student with a background in Neuroimaging/Physics/Biomedical Engineering in Amsterdam.
> The aim of the project is to optimize neurosurgical deep brain stimulation targeting using 3T and 7T scans.
> Compensation is according to the collective agreement (CAO-UMC) and amounts from EUR 2200,- gross per month in the first year to EUR 2818,- in the fourth year.
>
> For further information, please visit this website:
>
> www.academictransfer.com/28873
>
> Best wishes,
> Guido
> http://www.spinozacentre.nl/
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 10:25:57 +0100
> From: Ludovica Griffanti <[log in to unmask]>
> Subject: Re: rfmri functional connectivity
>
> Hi Javanray,
> I’m not sure whether you want to look at spatial differences in functional connectivity within (one or more) resting state networks or you want to compare the functional connectivity across networks.
> In the first case, see the MELODIC practical (http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/melodic/index.html) and the user guide for dual regression (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/DualRegression/UserGuide). Basically, after you set up the design matrix with your group comparison, the output of randomise (called within the dual regression script) is the answer to your question.
> In the second case, you will need the output of stage 1 of dual regression (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/DualRegression/UserGuide) to use FSLNets (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLNets), as also explained in the rfMRI practical (http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/rfMRIconnectivity/index.html). However, I would recommend you to read the MELODIC practical first anyway, as it provides the background for the rfMRI one.
>
> Hope that helps,
> Ludovica
>
> —
> Ludovica Griffanti, PhD
> Analysis Postdoctoral Research Assistant
> Oxford Centre for Functional MRI of the Brain (FMRIB)
> Nuffield Department of Clinical Neurosciences, University of Oxford
> John Radcliffe Hospital
> Oxford, OX3 9DU, UK
> email: [log in to unmask]
>
> On 8 Jul 2015, at 19:16, Mohammadali Javanray <[log in to unmask]> wrote:
>
>> Dear FSL experts,
>> Hi.
>>
>> I am calculating resting state functional connectivity. so far, I have preprocessed my data, ran MELODIC on it, done the dual regression and also the randomise.
>> what is the next step I have to do to calculate the functional connectivity and get to the point so I can compare the connectivity between my 2 groups of data (Controls and Autism). I have read the rfmri practical on FSL site, but I am not sure whether I am understanding it correctly or not, I would appreciate if you could kindly help me with that.
>>
>> Any clarification would be appreciated.
>> Thanks,
>> Javanray.
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 10:51:48 +0100
> From: SUBSCRIBE FSL Jay <[log in to unmask]>
> Subject: Re: PALM - MANOVA/MANCOVA option
>
> Hi Anderson,
>
> The following is the exact error i see in MATLAB terminal which keeps repeating in a loop for different RCOND
>
> =======================================
> In palm_backend at 1662
> In palm at 80
> Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 5.275093e-19.
>> In palm_backend>fasttsq at 2772
> In palm_backend>@(M,psi,res)fasttsq(M,psi,res,m,c,plm) at 942
> In palm_backend at 1662
> In palm at 80
> Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.181223e-18.
>> In palm_backend>fasttsq at 2772
> In palm_backend>@(M,psi,res)fasttsq(M,psi,res,m,c,plm) at 942
> In palm_backend at 1662
> In palm at 80
> Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 7.731050e-19.
>> In palm_backend>fasttsq at 2772
> In palm_backend>@(M,psi,res)fasttsq(M,psi,res,m,c,plm) at 942
> In palm_backend at 1662
> In palm at 80
> =======================================
>
> As you have suggested, when i remove one of MD, L1 or L23, it works fine and i dont get these warning messages. Hence, these warnings definitely are caused due to rank deficiency in GLM model.
>
> Thank you
> Jay
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 13:58:34 +0100
> From: Mohammadali Javanray <[log in to unmask]>
> Subject: Re: rfmri functional connectivity
>
> Dear Dr.Griffanti,
> Thanks for your helpful answer.
>
> I want to look at the spatial differences in functional connectivity within resting state networks to see the difference between Autism and Controls group,
> I have read the (http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/melodic/index.html) , it seems I have done the same procedure.
> Then I ran the following code to view the results from the dual regression analysis : (fslview $FSLDIR/data/standard/MNI152_T1_2mm groupmelodic_fix.ica/melodic_IC -l "Red-Yellow" -b 4,15 &) but don't know about the " -b 4,15" part, what does it do?
> Then I added the two files it says. Now I don't know whether I have to add all the 30 (dr_stage3_ic00??_tfce_corrp_tstat4.nii.gz) files I have, or not?
> The other question is, what does it show and how should I find out the difference between the two groups with this?
>
> Your clarification and collaboration are fully appreciated.
> Javanray.
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 15:33:59 +0100
> From: Mike <[log in to unmask]>
> Subject: topup necessary?
>
> Hi FSL experts,
>
> I'm a newbie of TBSS and have a simple question here. We used Siemens Prisma 3T to collect DTI and we only have the rawdata.nii, file.bvec, and file.bval. For TBSS, is TOPUP necessary? Or can I just start from eddy_correct?
>
> Mike
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 08:07:19 -0700
> From: Daniel Kim <[log in to unmask]>
> Subject: Re: FSL installation question
>
> Hi Sid
>
> All the binaries will be in the link to /usr/share/fsl/5.0 as well as the standard atlases and templates.
> Make sure your shell configures FSLDIR and calls the configuration files.
>
> Regards,
>
> Danny Kim
> On 2015-07-08, at 5:46 PM, Siddharth Srivastava wrote:
>
> Hi All,
> I am trying to install FSL on a Ubuntu machine (trusty thar), and following
> instructions from the fsl.fmrib.ox.ac.uk<http://fsl.fmrib.ox.ac.uk/> fsldownloads page. I am, however,
> having a harrowing time understanding the whole process for Ubuntu users.
> What I have done do far:
> - selected the Debian/Ubuntu section, which led me to the neurodebian page for fsl.
> - as instructed, I used apt-get fsl-complete
> - the installation finished without errors
> Seemed simple, but when I set out to find where fsl was installed, I saw both
> fsl4.1* and fsl5.0* in /usr/bin/, also there was a /usr/share/fsl with 4.0 and 5.0
> directories, and some links to /lib/fsl and /etc/ too.
>
> So, my questions are:
> - where is fsl installed after apt-get install
> - what is the best way to process after this? or is there another way?
> I can obviously try building from the source, but would rather avoid that...
>
> Thanks,
> Sid.
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 17:05:34 +0000
> From: "Alvarez Ferreira, Ivan" <[log in to unmask]>
> Subject: Re: topup necessary?
>
> Dear Mike,
>
> You can run EDDY as stand-alone, just leave out the appropriate flags. However, if you wish to correct for susceptibility-induced distortions, you should use TOPUP. EDDY alone will only correct for eddy currents/motion.
>
> Ivan Alvarez
>
>> On 9 Jul 2015, at 05:57 pm, "Mike" <[log in to unmask]> wrote:
>>
>> Hi FSL experts,
>>
>> I'm a newbie of TBSS and have a simple question here. We used Siemens Prisma 3T to collect DTI and we only have the rawdata.nii, file.bvec, and file.bval. For TBSS, is TOPUP necessary? Or can I just start from eddy_correct?
>>
>> Mike
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 17:07:32 +0000
> From: Jesper Andersson <[log in to unmask]>
> Subject: Re: topup necessary?
>
> Dear Mike,
>
>>
>> I'm a newbie of TBSS and have a simple question here. We used Siemens Prisma 3T to collect DTI and we only have the rawdata.nii, file.bvec, and file.bval. For TBSS, is TOPUP necessary? Or can I just start from eddy_correct?
>
> topup is not necessary, though probably beneficial. It doesn’t sound like you have the data needed for topup, so just skip it.
>
> Also, I would consider using eddy instead of eddy_correct.
>
> Jesper
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 12:21:46 -0500
> From: Eduardo Garza-Villarreal <[log in to unmask]>
> Subject: Re: topup necessary?
>
> Hi Mike
>
> Correction of geometric distortions are highly recommended, but you can
> still do eddy_correct without it as it is not a requirement as far as I'm
> aware. I recommend for future studies to add a Field Mapping sequence for
> using the TOPUP, as it takes seconds to collect and it adds to the quality
> of your data.
>
> You can read more about it DTI preprocessing here:
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594764/
> http://wiki.biac.duke.edu/lib/exe/fetch.php?media=biac:jones_etal_2012_the_do_s_and_don_ts_of_diffusion_mri.pdf
> http://www.diffusion-imaging.com/
>
> And a similar question was already asked in ResearchGate, here are the
> answers:
>
> https://www.researchgate.net/post/For_DTI_analysis_what_is_the_utility_of_obtaining_field_maps_Where_and_how_do_you_fit_them_into_your_image_processing_pipeline
>
>
> Hope this helps.
>
> Eduardo
>
>
> Eduardo A. Garza Villarreal, M.D., Ph.D.
>
>
> - Investigador, *Subdirección de Investigaciones Clínicas, Instituto
> Nacional de Psiquiatría.*
> - Catedrático, *Consejo Nacional de Ciencia y Tecnología (CONACYT).*
> - Investigador Asociado, *Center of Functionally Integrative
> Neuroscience, Universidad de Aarhus, Dinamarca.*
>
>
> On Thu, Jul 9, 2015 at 9:33 AM, Mike <[log in to unmask]> wrote:
>
>> Hi FSL experts,
>>
>> I'm a newbie of TBSS and have a simple question here. We used Siemens
>> Prisma 3T to collect DTI and we only have the rawdata.nii, file.bvec, and
>> file.bval. For TBSS, is TOPUP necessary? Or can I just start from
>> eddy_correct?
>>
>> Mike
>>
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 13:16:23 -0500
> From: Matt Glasser <[log in to unmask]>
> Subject: Re: topup necessary?
>
> To use topup you need phase reversed data (at least of the b0s), not a
> standard field map.
>
> Peace,
>
> Matt.
>
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
> Eduardo Garza-Villarreal <[log in to unmask]>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Thursday, July 9, 2015 at 12:21 PM
> To: <[log in to unmask]>
> Subject: Re: [FSL] topup necessary?
>
> Hi Mike
>
> Correction of geometric distortions are highly recommended, but you can
> still do eddy_correct without it as it is not a requirement as far as I'm
> aware. I recommend for future studies to add a Field Mapping sequence for
> using the TOPUP, as it takes seconds to collect and it adds to the quality
> of your data.
>
> You can read more about it DTI preprocessing here:
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594764/
> http://wiki.biac.duke.edu/lib/exe/fetch.php?media=biac:jones_etal_2012_the_d
> o_s_and_don_ts_of_diffusion_mri.pdf
> http://www.diffusion-imaging.com/
>
> And a similar question was already asked in ResearchGate, here are the
> answers:
>
> https://www.researchgate.net/post/For_DTI_analysis_what_is_the_utility_of_ob
> taining_field_maps_Where_and_how_do_you_fit_them_into_your_image_processing_
> pipeline
>
>
> Hope this helps.
>
> Eduardo
>
>
> Eduardo A. Garza Villarreal, M.D., Ph.D.
>
> * Investigador, Subdirección de Investigaciones Clínicas, Instituto Nacional
> de Psiquiatría.
> * Catedrático, Consejo Nacional de Ciencia y Tecnología (CONACYT).
> * Investigador Asociado, Center of Functionally Integrative Neuroscience,
> Universidad de Aarhus, Dinamarca.
>
> On Thu, Jul 9, 2015 at 9:33 AM, Mike <[log in to unmask]> wrote:
>> Hi FSL experts,
>>
>> I'm a newbie of TBSS and have a simple question here. We used Siemens Prisma
>> 3T to collect DTI and we only have the rawdata.nii, file.bvec, and file.bval.
>> For TBSS, is TOPUP necessary? Or can I just start from eddy_correct?
>>
>> Mike
>
>
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 19:38:40 +0100
> From: Kaitlyn Breiner <[log in to unmask]>
> Subject: Too much activation
>
> Hi FSL users and experts,
>
> I'm finding too much activation for one contrast in one subject. I ran a first-level analysis to assess differences between two time points (E1 and E2). The poststats report revealed virtually no activation for E1 v Baseline (not too surprising), but the complete opposite for E2 v Baseline across the whole brain. E2 v E1 is worse, with nearly the entire brain showing activation. A few things are worth noting:
>
> 1) There are 4 trials that are modeled for each event.
> 2) This exact contrast was used for 26 other subjects, and twice more for different contrasts for this subject and did not reveal this problem.
> 3) Registration is good.
> 4) The onset files look fine, and after running the first-level analysis on this contrast again, the same issue arose.
>
> There appears to be some motion that occurs around the time points of these events, but I'm doubtful whether that's the cause. Any help/advice would be greatly appreciated!
>
> Kaitlyn
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 19:52:19 +0100
> From: Mike <[log in to unmask]>
> Subject: Re: topup necessary?
>
> Thanks for all your replies. One more qestion: if I do collect field map image, can I use it to correct my DWI data? And can this replace topup?
>
> Mike
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 14:02:44 -0500
> From: Eduardo Garza-Villarreal <[log in to unmask]>
> Subject: Re: topup necessary?
>
> Hi Mike,
>
> As Matt pointed out, for TOPUP it is not a standard field mapping, and it
> is easier to acquire. If you want a regular field mapping sequence I can't
> help you with that but there is plenty of information out there.
>
> The easiest will be to copy the same DTI sequence you have, but changing it
> so it only acquires a few b0 volumes with the reverse blip (if it was
> acquired AP, then acquire it PA).
>
> I don't use a Siemens scanner, but in my Phillips I run a sequence with
> about 4 b0 and I have to run the minimum directions (6) in the opposite
> direction.
>
> Eduardo
>
>
>
>
> Eduardo A. Garza Villarreal, M.D., Ph.D.
>
>
> - Investigador, *Subdirección de Investigaciones Clínicas, Instituto
> Nacional de Psiquiatría.*
> - Catedrático, *Consejo Nacional de Ciencia y Tecnología (CONACYT).*
> - Investigador Asociado, *Center of Functionally Integrative
> Neuroscience, Universidad de Aarhus, Dinamarca.*
>
>
> On Thu, Jul 9, 2015 at 1:52 PM, Mike <[log in to unmask]> wrote:
>
>> Thanks for all your replies. One more qestion: if I do collect field map
>> image, can I use it to correct my DWI data? And can this replace topup?
>>
>> Mike
>>
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 14:04:43 -0500
> From: Matt Glasser <[log in to unmask]>
> Subject: Re: topup necessary?
>
> Yes, but topup is the recommended approach over a field map for diffusion
> data.
>
> Peace,
>
> Matt.
>
> On 7/9/15, 1:52 PM, "FSL - FMRIB's Software Library on behalf of Mike"
> <[log in to unmask] on behalf of [log in to unmask]> wrote:
>
>> Thanks for all your replies. One more qestion: if I do collect field map
>> image, can I use it to correct my DWI data? And can this replace topup?
>>
>> Mike
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 20:31:46 +0100
> From: Danielle Miller <[log in to unmask]>
> Subject: Feat Z Max values
>
> Hi FSL experts,
>
> Are the Z max values presented in Feat output for clusters absolute values? For anticorrelations I am getting positive z peak values.
>
> Thanks,
> Danielle
>
> ------------------------------
>
> Date: Thu, 9 Jul 2015 20:47:44 +0100
> From: Keren Lesinger <[log in to unmask]>
> Subject: Re: FEAT second level analysis with standard space from ants
>
> Thanks Katie, I tried to create all the files you mentioned. now when I ran the copes I at least don't get the box with registration error, but I get a simmilar error to the error which ocurred when I ran the second level analysis with feat directories as inputs.I would like to make sure my first level analysis was defined appropriately similar to your , did u ran registration stage in the first level analysis? can you walk me through your stages in the first level analysis ?
>
> Thanks!
>
> Keren
>
> ------------------------------
>
> End of FSL Digest - 8 Jul 2015 to 9 Jul 2015 (#2015-9)
> ******************************************************
>
--
Beste Grüße
Annette Winkelmann
---
Humboldt-Universitaet zu Berlin
Berlin School of Mind and Brain
Annette Winkelmann, M.A.
Managing Director/Geschaeftsfuehrerin
Unter den Linden 6
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