Dear Siewmin,
> 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
This far all looks good as far as I can see.
> (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
This bit I would do differently. I would combine the linear FA->T1
transform with the non-linear T1->MNI transform, and then invert that
combined warp. I.e. I would do
convertwarp --ref=MNI152lin_T1_1mm_brain --out=FA2MNI_transform
--premat=A2T1.mat --warp1=my_nonlinear_transf
invwarp --ref=Image_FA_brain --warp=FA2MNI_transform --out=MNI2FA_transform
> 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?
Yes.
> 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
I would need to understand what you are attempting to do here. By choosing
a template with higher resolution (1mm) you will incur longer execution
time and greater memory demands. At the same time you have chosen a
template that has much less relevant information at high resolution (since
the average of the linearly registered brains is very blurred). What you
are suggesting makes little sense to me off the top of my head, and maybe
if I knew your motivation for this choice I could help you better.
> 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?
See my suggestion above.
> 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 ?
Ohh, I see now why you want to use the linear template. I still think it
makes more sense to use the non-linear template. That would allow you to
obtain a better registration of your subject into standard space, and
assuming that there is no bias between the linear and the non-linear
templates it should still be valid to transfer your ROI's from the linear
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?
No. If there were a way to assess the quality of registration we would use
that to drive the registration.
>
> 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)?
No, not as long as it is projected down onto a diffeomorphic transform
prior to inverting it. This should be done when using the default settings
of fnirt.
Good Luck Jesper
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