Hi everyone again,

I transformed the surfaces from fsaverage to subject's space fine but I got stuck on the subcortical volume transformation. I apologize, as this is probably basic, still I run out of ideas...

So, my problem is to transform the 'sig.nii.gz' map (of the subcortical activations from standard FS-Fast pipeline) from the mni305 to the orig space of the subject.
I found the 'talairach.xfm' transform from the orig->MNI space, but I didn't find the reversed registration file (if it exists anywhere, please let me know). So I created the back-registration file with bbregister:
bbregister --s Sub001 --mov ~/Freesurfer/subjects/fsaverage/mri/mni305.cor.mgz --T1 --init-fsl --reg mni2subject.dat

I checked both with the tkregister2 and with the freeview that the orig.mgz and the mni305 with applied registration align. So I tried to apply this registration parameters to the sig.nii.gz with mri_vol2vol:
mri_vol2vol --mov sig.nii.gz --targ ~/Freesurfer/subjects/Sub001/mri/orig.mgz --reg mni2subject.dat --o sig.native.nii.gz
But the output 'sig.native.nii.gz' does not align with the 'orig.mgz' of the subject.

What's more, the prompt on the terminal suggests to check for the registration with:
tkregister2 --mov sig.native.nii.gz --targ /home/pati/Freesurfer/subjects/Sub001/mri/orig.mgz --reg sig.native.nii.gz.reg

as if it was the output file (sig.native...) being moved with the registration parameters. So I assume that I've messed up something?

So all in end I have a strange situation when sig.nii aligns with MNI, MNI with registration aligns with orig.mgz, but sig.nii with registration does not align with orig.mgz.
I will appreciate any ideas of - how to deal with the problem. Also, as it is highly possible, maybe there's an easier way of transforming the volume output of fs-fast back to orig subject space?

I'm running Freesurfer 5.3 on Gentoo Linux.

Best regards,
Patrycja

2017-04-26 23:20 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
glad it worked out :)

On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:

Hi Bruce,

thanks for a quick reply! mri_surf2surf worked fine just with specifying the
target and source subjects, no registration file needed - much appreciated
:)

Best regards,
Patrycja

2017-04-26 22:51 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Patrycja

      the standard transform we use to fsaverage coordinates is
      surface-based (spherical). If you sample your EPI onto the
      surface, I believe you can use mri_surf2surf to transfer it from
      subject to fsaverage

      cheers
      Bruce
      On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:

            Hello FS experts,

            I have a question regarding FS-Fast processing. I
            have performed
            (successfully!)  an FS-Fast single subject analysis.
            The results look fine
            in the fsaverage space, but I'm interested in
            viewing them in the subject
            space.

            Are the registration files used along the processing
            pipeline
            (EPI->T1->fsaverage) stored anywhere (so far I only
            found the EPI->T1 and
            T1->talairach files), so I can use them? Or do I
            need to create new
            registration files (bbregister/tkregister2)?

            Best regards,
            Patrycja


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