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FSL  May 2009

FSL May 2009

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Subject:

Re: choice of registration and MNI template

From:

Siew-Min Gan <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 20 May 2009 21:42:59 +1000

Content-Type:

text/plain

Parts/Attachments:

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text/plain (459 lines)

>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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