>Thanks. I've attached the 12dof output matrix run on avscale below. With
the commands you gave me, I tried these fslmaths commands before. For the
first command, I get a white box in fslview ( nobrain). With the second
command, I get a binary image with the brain as 0 and the nonbrain tissue
as 1. I'm not sure why, hence i did the calculations with matlab. Thanks
again.
Rotation & Translation Matrix:
0.999976 0.005551 -0.004088 -7.866150
-0.006757 0.907013 -0.421049 13.451900
0.001371 0.421067 0.907028 -18.613500
0.000000 0.000000 0.000000 1.000000
Scales (x,y,z) = 1.915426 1.947678 1.910669
Skews (xy,xz,yz) = 0.001418 0.003214 0.027073
Average scaling = 1.92459
Determinant = 7.128
Left-Right orientation: preserved
Forward half transform =
1.383981 0.005175 -0.000129 -3.308535
-0.004572 1.362760 -0.279752 4.693886
0.001458 0.300895 1.353795 -8.490392
0.000000 0.000000 0.000000 1.000000
Backward half transform =
0.722547 -0.002377 -0.000530 2.397223
0.002173 0.704262 0.144634 -2.070535
-0.001260 -0.156453 0.703926 6.706810
0.000000 0.000000 0.000000 1.000000
Hi,
>
> I suspect that the problem is these more extreme values
> around the brain edge. Are you expecting any true values
> to be less than 0? If not, then it would help to remove the
> negative values. You can repeat the same calculation in
> fslmaths with:
> fslmaths mtoff -sub mton -div mtoff mtr_image
> or include a lower cutoff at zero as well with:
> fslmaths mtoff -sub mton -div mtoff -max 0 mtr_image
>
> Try this and see if you can get a 6 DOF registration to
> work with this image.
>
> As for the avscale - you seem to have run it on a 6 DOF output.
> Can you please run it on the 12 DOF output matrix (in the
> same way that you did - no other options are required) and
> send me the output then.
>
> All the best,
> Mark
>
> On 21 May 2009, at 11:52, Siew-Min Gan wrote:
>
>>> Thanks. There's scaling and skewing of the MTR image registered to
>>> the
>> same subjects T1 (both deskulled). There is some negative value
>> intensities around the edge of the brain of the MTR image. When I try
>> fslstats MTR_brain.nii.gz -R, I get -72.000000 1.000000. The
>> Magnetisation Transfer Imaging Ratio image is derived from [(mtoff
>> image-mton images)/mt_off image] in with MATLAB. Is there a fsl
>> command
>> that can perform this function that I can check if I've done the maths
>> correctly, although I'm pretty sure the images are subtracted and
>> divided
>> correctly. I can't get a perfectly deskulled MTR image with BET
>> without
>> losing some of the brain itself, and the best MTR image betted would
>> still have 1-2 pixels of nonbrain around it.
>>
>>
>> When I type avscale, I get
>> avscale [--allparams/--inverteddies] matrixfile [non-reference-
>> volume].
>> What does [--allparams/--inverteddies] mean, and is the
>> [non-reference-volume] my betted MTR image?
>>
>> i typed avscale MTR2T1.mat and this is my output below. Please let me
>> know if this is not what you need. thanks
>>
>> Siewmin
>>
>> Rotation & Translation Matrix:
>> 0.995794 -0.021164 -0.089148 7.369500
>> 0.060188 0.884693 0.462272 16.040700
>> 0.069085 -0.465693 0.882246 76.415500
>> 0.000000 0.000000 0.000000 1.000000
>>
>> Scales (x,y,z) = 1.000000 1.000000 1.000000
>>
>> Skews (xy,xz,yz) = 0.000000 -0.000000 0.000000
>>
>> Average scaling = 1
>>
>> Determinant = 1
>> Left-Right orientation: preserved
>>
>> Forward half transform =
>> 0.998933 -0.016017 -0.043333 4.561216
>> 0.025922 0.970733 0.238760 3.341746
>> 0.038240 -0.239628 0.970111 39.105334
>> 0.000000 0.000000 0.000000 1.000000
>>
>> Backward half transform =
>> 0.998932 0.025922 0.038240 -6.138365
>> -0.016017 0.970733 -0.239628 6.199851
>> -0.043333 0.238760 0.970112 -38.536765
>> 0.000000 0.000000 0.000000 1.000000
>>
>> Hi,
>>>
>>> I assume MTR is Magnetisation Transfer Ratio - but this doesn't
>>> explain why 12 dof works while 6 dof fails. I assume they are of
>>> the same subject - right?
>>>
>>> Is there anything unusual with the intensities around the edge of
>>> the brain? And does the 12 dof result do a lot of scaling or
>>> skewing?
>>> Can you run avscale on the transformation matrix from FLIRT and
>>> send us the output?
>>>
>>> All the best,
>>> Mark
>>>
>>> On 20 May 2009, at 22:12, Matt Glasser wrote:
>>>
>>>> What is MTR, I don't think I know that acronym.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> -----Original Message-----
>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>>> Behalf
>>>> Of Siew-Min Gan
>>>> Sent: Wednesday, May 20, 2009 6:43 AM
>>>> To: [log in to unmask]
>>>> Subject: Re: [FSL] choice of registration and MNI template
>>>>
>>>>> Understood. Thanks for your explaination.
>>>>
>>>> I noticed that with registerering MTR deskulled brains to T1, I can
>>>> only
>>>> do so with flirt with 12dof affine and not 6 or 9 dof. May I ask why
>>>> does
>>>> 6DOF works for undistorted fa but not for MTR images?
>>>>
>>>> Thanks
>>>>
>>>> Siewmin
>>>>
>>>> I'm sorry, I think I misunderstood you somewhere along the way and
>>>> that is
>>>>> the source of our confusion. You are correct that the 1mm and 2mm
>>>>> templates
>>>>> have different matrix sizes (this is what I didn't realize you were
>>>>> referring to). I thought you had some other version of the MNI
>>>>> template
>>>>> that had more empty space around it (a bigger FOV). The FOV
>>>>> actually is
>>>>> exactly the same, it is just the matrix that is larger in the 1mm
>>>>> (as it
>>>>> divides the same FOV into smaller voxels). There will be no
>>>>> translational
>>>>> difference in the images (I just verified this by resampling the
>>>>> 2mm
>>>>> template to the 1mm template using an identity matrix). If your
>>>>> images
>>>>> had
>>>>> different FOVs, rather than different matrix sizes, you cannot
>>>>> necessarily
>>>>> just resample the images with an identity matrix.
>>>>>
>>>>> If you look carefully in that config file, you will see that the
>>>>> last
>>>>> subsampling step is 2 rather than 1 (and hence the highest
>>>>> resolution
>>>>> reference image used is 2mm). Since you want your transform to be
>>>>> from
>>>>> the
>>>>> 1mm MNI space to the 1mm T1 space (and then the FA), you could just
>>>>> edit
>>>>> the
>>>>> config file to use the 1mm nonlinearly generated template and
>>>>> double the
>>>>> numbers in the --subsamp option (i.e. --subsamp=4,4,2,2,1,1 becomes
>>>>> --subsamp=8,8,4,4,2,2). This will give you what you want without
>>>>> taking
>>>>> an
>>>>> inordinate amount of time.
>>>>>
>>>>> Hope this clarifies everything.
>>>>>
>>>>> Peace,
>>>>>
>>>>> Matt.
>>>>>
>>>>> -----Original Message-----
>>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>>>> Behalf
>>>>> Of Siew-Min Gan
>>>>> Sent: Tuesday, May 19, 2009 4:50 PM
>>>>> To: [log in to unmask]
>>>>> Subject: Re: [FSL] choice of registration and MNI template
>>>>>
>>>>>> Hi Matt,
>>>>> sorry I'm a bit unclear now. Do you mean there
>>>>> might be
>>>>> translational difference in my normalised FA if I use a
>>>>> 2mm or 1mm MNI template ( with different FOV) for
>>>>> registration? Is that due to the interpolation when the
>>>>> normalised FA is resampled? If I'm doing the registration
>>>>> FA2T1 and T12MNI, so I can get the inverse matrix to
>>>>> transfer the template rois back to my FA native space,
>>>>> would this translation still occur when the binary rois
>>>>> are interpolated via nearest neighbour (i.e the rois
>>>>> positioning would differ by translation when placed in
>>>>> the native FA space depending on which MNI template I
>>>>> use)?
>>>>>
>>>>> The fMRIB config file FA_2_FMRIB58_1mm.cnf uses the 1mm. Please
>>>>> correct me
>>>>> if I'm wrong.
>>>>>
>>>>> thanks
>>>>>
>>>>> Siewmin
>>>>>
>>>>> On the first point, I think you do, but am not 100% sure. The
>>>>> differences
>>>>>> would only be translational. For the nonlinear registration, the
>>>>>> warp
>>>>>> fields are on the order of 8-10mm in resolution so it never
>>>>>> makes a
>>>>>> difference in the warpfield to register at a higher resolution.
>>>>>> What it
>>>>>> does make a difference in is processing time and resource usage.
>>>>>> Thus,
>>>>>> in
>>>>>> none of the fMRIB generated config files is a reference image used
>>>>>> with
>>>>>> less
>>>>>> than a 2mm resolution (or a subsampling step that makes the image
>>>>>> 2mm
>>>>>> internally).
>>>>>>
>>>>>> Peace,
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>>>>>> On
>>>>>> Behalf
>>>>>> Of Siew-Min Gan
>>>>>> Sent: Tuesday, May 19, 2009 3:15 PM
>>>>>> To: [log in to unmask]
>>>>>> Subject: Re: [FSL] choice of registration and MNI template
>>>>>>
>>>>>>> Thanks for your reply.
>>>>>> Can I clarify with you two points? You mentioned I need to take
>>>>>> into
>>>>>> account the FOVs in the applywarp step, do you just mean that my
>>>>>> transformed FA in MNI space will take on the FOV of the MNI
>>>>>> template
>>>>>> that
>>>>>> I'm registerering to?
>>>>>> Secondly, my FA image is 2mm isotropic, my T1 image is 1mm
>>>>>> isotropic.
>>>>>> For
>>>>>> nonlinear registration of my T1 image to the MNI template, do you
>>>>>> mean
>>>>>> it
>>>>>> makes no difference for the quality of registration whether I
>>>>>> choose the
>>>>>> 1mm or the 2mm template MNI template? I.e it doesn't make better
>>>>>> registration if the target image (MNI brain) is same resolution as
>>>>>> source
>>>>>> image (my T1)?
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Siewmin
>>>>>>
>>>>>> It really is fine to do the registration in two steps. You just
>>>>>> don't
>>>>>>> want
>>>>>>> to resample your data (i.e. your ROIs) multiple times, so you can
>>>>>>> use
>>>>>>> the
>>>>>>> options of applywarp to do your resampling in a single step. If,
>>>>>>> for
>>>>>>> some
>>>>>>> reason, you wanted to do quantitative analysis on the FA in MNI
>>>>>>> space,
>>>>>>> it
>>>>>>> would be better register the FA to the T1 and the T1 to the MNI
>>>>>>> and
>>>>>>> then
>>>>>>> use
>>>>>>> apply warp to move the FA to MNI space in one step. Does this
>>>>>>> make
>>>>>>> sense?
>>>>>>>
>>>>>>> I am not sure what the best way to deal with the different FOVs.
>>>>>>> One
>>>>>>> could
>>>>>>> simply "register" the two templates together using 3 DOF
>>>>>>> (translations
>>>>>>> only), however maybe there is a more elegant way... (although
>>>>>>> voxel
>>>>>>> coordinates are different, mm coordinates will be the same in
>>>>>>> both
>>>>>>> templates). The FOVs will not make a difference for the quality
>>>>>>> of the
>>>>>>> registrations, but you might need to take them into account for
>>>>>>> the
>>>>>>> applywarp step.
>>>>>>>
>>>>>>> Peace,
>>>>>>>
>>>>>>> Matt.
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: FSL - FMRIB's Software Library
>>>>>>> [mailto:[log in to unmask]] On
>>>>>>> Behalf
>>>>>>> Of Siew-Min Gan
>>>>>>> Sent: Monday, May 18, 2009 10:35 AM
>>>>>>> To: [log in to unmask]
>>>>>>> Subject: Re: [FSL] choice of registration and MNI template
>>>>>>>
>>>>>>>> Thanks.
>>>>>>>
>>>>>>> Sory I wasn't clear with the 3rd Question. The two ways mentioned
>>>>>>> have
>>>>>>> the
>>>>>>> similiarity of first registering FA to T1 (linearly) for the same
>>>>>>> subject.
>>>>>>> The difference is with the 1st way:
>>>>>>> after the linear registration of FA2T1, I then nonlinearly
>>>>>>> register T1
>>>>>>> from it's T1 native space directly to MNI standard space. Hence
>>>>>>> Fa
>>>>>>> image
>>>>>>> is moved twice to get into the standard space (Fa2T1 and T12MNI).
>>>>>>> Likewise
>>>>>>> the atlas rois from standard space is transformed back to the
>>>>>>> native FA
>>>>>>> image via two inverse matrices ( of FA2T1 and T12MNI)
>>>>>>> With the second way
>>>>>>> 2) after getting the linear regisration matrix of FA2T1, I apply
>>>>>>> the
>>>>>>> inverse of the registration matrix of FA2T1 on the T1 image,
>>>>>>> moving T1
>>>>>>> onto FA image space. I then nonlinearly register this registered
>>>>>>> T1
>>>>>>> (which is now in FA space) onto MNI standard space. This is
>>>>>>> different
>>>>>>> to
>>>>>>> above where the T1 was registered from it's native space.
>>>>>>> Hence, in
>>>>>>> contrast to above, the Fa image would only need to move once to
>>>>>>> get
>>>>>>> into
>>>>>>> the standard space via the nonlinear transformation matrix of the
>>>>>>> registeredT1to MNI.Likewise the atlas rois from the standard
>>>>>>> space is
>>>>>>> transformed back to the native FA image via only one inverse
>>>>>>> matrix (
>>>>>>> of
>>>>>>> the RegisteredT12MNI.
>>>>>>>
>>>>>>> I wonder which one would be more accurate to transform the roi
>>>>>>> back to
>>>>>>> the
>>>>>>> native FA space ?
>>>>>>>
>>>>>>> With the choice of the MNI template, the ROIs of the atlas are
>>>>>>> created
>>>>>>> and
>>>>>>> drawn on an average dti map which is normalised to the space of
>>>>>>> the
>>>>>>> linearly created MNI152 182x218x182 1mm atlas. The MNI152 2mm
>>>>>>> atlas
>>>>>>> used
>>>>>>> in the provided cnf file is nonlinearly created and is of
>>>>>>> dimension i.e
>>>>>>> 91
>>>>>>> x 109 x91 . If the dimensions and resolution are not important to
>>>>>>> get
>>>>>>> the
>>>>>>> registration matrix to backtransform the standard space rois to
>>>>>>> native
>>>>>>> fa
>>>>>>> image, but would there be some dissimiliarity between the
>>>>>>> linearly
>>>>>>> created
>>>>>>> and the nonlinearly created MNI152 template? Hence, I thought it
>>>>>>> would
>>>>>>> be
>>>>>>> more "accurate" to register to the linearly created MNI template
>>>>>>> which
>>>>>>> is
>>>>>>> used when creating the rois, although this would be at the
>>>>>>> expense of
>>>>>>> the
>>>>>>> registration? Please correct me if I'm wrong.
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Siewmin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> You should use the default file in the T1_2_MNI152_2mm.cnf as
>>>>>>> that will
>>>>>>>> give
>>>>>>>> the best results. That config file is properly tuned to give
>>>>>>>> optimal
>>>>>>>> T1
>>>>>>>> to
>>>>>>>> MNI template registrations. Why use a worse quality reference
>>>>>>>> image
>>>>>>>> (the
>>>>>>>> linear template) with higher resolution (much longer processing
>>>>>>>> time
>>>>>>>> and
>>>>>>>> higher resource usage for no benefit in registration quality)?
>>>>>>>>
>>>>>>>> Your commands look correct to me.
>>>>>>>>
>>>>>>>> 1. Yes
>>>>>>>>
>>>>>>>> 2. See above you shouldn't modify the config file.
>>>>>>>>
>>>>>>>> 3. I am having some difficulty following you. So long as you
>>>>>>>> have
>>>>>>>> transformations describing FA -> T1 and T1 -> MNI, you can move
>>>>>>>> anything
>>>>>>>> you
>>>>>>>> want from FA to MNI or MNI to FA. Applywarp will only resample
>>>>>>>> the
>>>>>>>> images
>>>>>>>> once, even if you include both a linear and nonlinear
>>>>>>>> transformation
>>>>>>>> (in
>>>>>>>> fact you can include up to two linear transformations, one
>>>>>>>> before and
>>>>>>>> one
>>>>>>>> after the nonlinear one) so long as you give everything in one
>>>>>>>> commandline.
>>>>>>>> You can also combine linear and nonlinear transformations with
>>>>>>>> convertwarp.
>>>>>>>>
>>>>>>>>
>>>>>>>> 4. Again I don't think you should be using the linearly derived
>>>>>>>> templates.
>>>>>>>>
>>>>>>>> I'm not sure of the best answer to your last two questions.
>>>>>>>>
>>>>>>>> Peace,
>>>>>>>>
>>>>>>>> Matt.
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>>>>>>>> On
>>>>>>>> Behalf
>>>>>>>> Of Siewmin Gan
>>>>>>>> Sent: Monday, May 18, 2009 8:00 AM
>>>>>>>> To: [log in to unmask]
>>>>>>>> Subject: [FSL] choice of registration and MNI template
>>>>>>>>
>>>>>>>> Hi, I have a few questions about trying fnirt to register fa and
>>>>>>>> other
>>>>>>>> scalar maps to the
>>>>>>>> MNI template, so I can use the invert transformations to put the
>>>>>>>> rois
>>>>>>>> of
>>>>>>>> the
>>>>>>>> white matter
>>>>>>>> atlas back onto the native fa and scalar maps. Apologies for the
>>>>>>>> long
>>>>>>>> questions.
>>>>>>>>
>>>>>>>> I performed linear 6DOF registration of subjects FA to their T1,
>>>>>>>> and
>>>>>>>> linear
>>>>>>>> followed by
>>>>>>>> non_linear registration of T1 to MNI152. The fa and scalar maps
>>>>>>>> are
>>>>>>>> calculated from 4D
>>>>>>>> DWI with B0 unwarping/undistortion performed. These maps are 2mm
>>>>>>>> isotropic
>>>>>>>> and the
>>>>>>>> T1 images of the subjects are 1mm isotropic. The MNI template
>>>>>>>> chosen
>>>>>>>> is
>>>>>>>> the
>>>>>>>> MNI_linear
>>>>>>>> template 1mm. I did this following similiar steps to the 2nd
>>>>>>>> fnirt
>>>>>>>> example
>>>>>>>> script on the
>>>>>>>> fnirt website (i.e fmri to MNI via T1) and with slight
>>>>>>>> modification of
>>>>>>>> the
>>>>>>>> T1_2_MNI152_2mm.cnf. May I ask if the following commands are the
>>>>>>>> right
>>>>>>>> way
>>>>>>>> and
>>>>>>>> quickest way to "concantenate" the two inverse linear T12FA
>>>>>>>> matrix and
>>>>>>>> nonlinear MNI2T1
>>>>>>>> warp coefficient to transform binary rois from MNI to the native
>>>>>>>> FA
>>>>>>>> space?
>>>>>>>> I have also
>>>>>>>> listed my questions below about the choice of registration,
>>>>>>>> template
>>>>>>>> and
>>>>>>>> using these
>>>>>>>> appropriate parameters in the config file:
>>>>>>>>
>>>>>>>> T1_brain and Image_FA_brain (betted) The Image_FA I have is
>>>>>>>> betted so
>>>>>>>> I
>>>>>>>> don't have a FA
>>>>>>>> image with skull.
>>>>>>>>
>>>>>>>> flirt -ref T1_brain -in Image_FA_brain -out FA2T1_brain -omat
>>>>>>>> FA2T1.mat;
>>>>>>>> flirt -ref MNI152lin_T1_1mm_brain -in T1_brain -omat
>>>>>>>> my_affine_transf.mat;
>>>>>>>> fnirt --in=T1 --aff=my_affine_transf.mat --
>>>>>>>> cout=my_nonlinear_transf --
>>>>>>>> config=T1_2_MNI152lin_1mm.cnf;
>>>>>>>> applywarp --ref=MNI152lin_T1_1mm --in=Image_FA_brain
>>>>>>>> --warp=my_nonlinear_transf -
>>>>>>>> -premat=FA2T1.mat --out=my_warped_fa2mni_1mm
>>>>>>>>
>>>>>>>> (applying inverse matrix to place ROI from MNI to FA native
>>>>>>>> space)
>>>>>>>> convert_xfm -omat T12FA.mat -inverse FA2T1.mat
>>>>>>>> invwarp --ref=T1.nii.gz --warp=my_nonlinear_transf.nii.gz
>>>>>>>> --out=nonlinear_MNI2T1
>>>>>>>> applywarp --ref=Image_FA_brain --in=ROIs_in_MNI_space
>>>>>>>> --warp=nonlinear_MNI2T1 --
>>>>>>>> postmat=T12FA.mat out=ROIs_in_FAnative_space --interp=nn
>>>>>>>>
>>>>>>>>
>>>>>>>> 1. Is it ok that I use a betted FA image all the way in these
>>>>>>>> steps,
>>>>>>>> as
>>>>>>>> long
>>>>>>>> as the T1
>>>>>>>> image used in FNIRT is the original T1 with skull on?
>>>>>>>>
>>>>>>>> 2. I use the MNI152_lin_1mm template with slight modifications
>>>>>>>> to
>>>>>>>> T1_2_MNI152_2mm.cnf ( renaming it T1_2_MNI142lin_1mm.cnf ). The
>>>>>>>> MNItemplate
>>>>>>>> now
>>>>>>>> chosen is a lot smoother, is 1mm and of different intensity to
>>>>>>>> the
>>>>>>>> other
>>>>>>>> MNI
>>>>>>>> template
>>>>>>>> used in T1_2_MNI152_2mm.cnf). Apart from modifying the cnf
>>>>>>>> file by
>>>>>>>> changing
>>>>>>>> the MNI
>>>>>>>> template to the linear 1mm template, and the corresponding brain
>>>>>>>> mask
>>>>>>>> ,
>>>>>>>> which other
>>>>>>>> parameters would be important to change (my T1 and the
>>>>>>>> MNIlin_1mm are
>>>>>>>> both
>>>>>>>> 1mm in
>>>>>>>> resolution? Would there be any recommendations you suggest for
>>>>>>>> the
>>>>>>>> some
>>>>>>>> of
>>>>>>>> parameters in the config file in this circumstance: The current
>>>>>>>> settings
>>>>>>>> in
>>>>>>>> the
>>>>>>>> T1_2_MNI152_2mm config files are
>>>>>>>>
>>>>>>>> subsamp:4,4,2,2,1,1
>>>>>>>> infwhm: 8,6,5,4.5,3,2
>>>>>>>> refwhm:8,6,5,4,2,0
>>>>>>>> lambda:300,150,100,50,40,30
>>>>>>>> intorder:5
>>>>>>>> biasres: 50 50 50
>>>>>>>>
>>>>>>>> 3. If I perform registration of image fa -->t1 -->to mni,
>>>>>>>> without
>>>>>>>> including
>>>>>>>> the -out in the
>>>>>>>> command line, the fa imagehas to be resampled once when
>>>>>>>> nonlinear
>>>>>>>> transformation to
>>>>>>>> the MNI 1mm space is performed. Alternatively, I can use the
>>>>>>>> inverse
>>>>>>>> matrix
>>>>>>>> of
>>>>>>>> FA2T1.mat (i.e T12FA.mat) on T1. This will register T1 to FA
>>>>>>>> followed
>>>>>>>> by
>>>>>>>> nonlinear
>>>>>>>> transformation of this registeredT1 to the MNI template to get
>>>>>>>> the
>>>>>>>> my_nonlinear_transf
>>>>>>>> matrix file of the T1(inFA native space) to MNI, which I can use
>>>>>>>> to
>>>>>>>> transform FA to MNI in
>>>>>>>> one step. With the 1st method, the rois of the white matter
>>>>>>>> template
>>>>>>>> would
>>>>>>>> be
>>>>>>>> transformed onto the raw FA image using the inverse of
>>>>>>>> my_nonlinear_transf
>>>>>>>> matrix and
>>>>>>>> FA2T1.mat as written in the command line above. With the second
>>>>>>>> method,
>>>>>>>> only
>>>>>>>> the
>>>>>>>> inverse of my_nonlinear_transf matrix would be used, without
>>>>>>>> requiring
>>>>>>>> the
>>>>>>>> postmat
>>>>>>>> T12FA.mat. With the Fa_image contrast and resolution, which way
>>>>>>>> would
>>>>>>>> be
>>>>>>>> more
>>>>>>>> precise/accurate to i) register or normalise ( register and
>>>>>>>> resample
>>>>>>>> FA
>>>>>>>> images to MNI
>>>>>>>> template) and ii) back-register the rois (by neighbouring
>>>>>>>> interpolation)from
>>>>>>>> the template
>>>>>>>> to the raw space of the FA image?
>>>>>>>>
>>>>>>>> 4. The rois of the white matter atlas is created when
>>>>>>>> normalising to
>>>>>>>> the
>>>>>>>> MNI152_lin_1mm
>>>>>>>> template and not the MNI152 _1mm (the non linear template which
>>>>>>>> has a
>>>>>>>> higher
>>>>>>>>
>>>>>>>> resolution). If I want to invert transform the rois of the atlas
>>>>>>>> in
>>>>>>>> MNI
>>>>>>>> space to the native
>>>>>>>> space of the fa images, would it be right to use the
>>>>>>>> MNI152_lin_1mm
>>>>>>>> template
>>>>>>>> to get the
>>>>>>>> transformation matrices(because of how the rois of the atlas has
>>>>>>>> been
>>>>>>>> created), even
>>>>>>>> though it is of poorer resolution than the other nonlinear MNI
>>>>>>>> template
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>> 5. Is there any output from running the flirt and fnirt that can
>>>>>>>> be
>>>>>>>> used
>>>>>>>> to
>>>>>>>> get a measure
>>>>>>>> of the precision in the registration methods (apart from visual
>>>>>>>> inspections), or there a
>>>>>>>> paper of fnirt that mentioned the precision of fnirt? I read
>>>>>>>> that one
>>>>>>>> way
>>>>>>>> to
>>>>>>>> quantitate the
>>>>>>>> registration quality of the rois apart from visual inspection is
>>>>>>>> assess
>>>>>>>> the
>>>>>>>> amount of
>>>>>>>> displacement of x,y, z coordinated of defined landmarks from the
>>>>>>>> MNI
>>>>>>>> space
>>>>>>>> when they
>>>>>>>> are transferred to the normalised FA images?
>>>>>>>>
>>>>>>>> 6. Lastly, on the fnirt website, it mentioned that fnirt method
>>>>>>>> is not
>>>>>>>> diffeomorphic by
>>>>>>>> consruction with some explainations of the difference. Would
>>>>>>>> that
>>>>>>>> matter
>>>>>>>> in
>>>>>>>> my case
>>>>>>>> whether I use a diffeomorphic by construction method or not for
>>>>>>>> the
>>>>>>>> purpose
>>>>>>>> I'm trying to
>>>>>>>> achieve here(i.e to try as best to register binary rois from the
>>>>>>>> atlas
>>>>>>>> to
>>>>>>>> the native fa
>>>>>>>> space)?
>>>>>>>>
>>>>>>>> Many thanks for your kind patience.
>>>>>>>>
>>>>>>>> Siewmin
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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