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 <fis...@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 <fis...@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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
