>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
>>>
>>
>
