If you just want to view the result on the native anatomy, you can use tkmedit-sess with the -self option. You can do the same thing with tksurfer-sess to view the surface-based data on the subject's own surface instead of fsaverage. If this is something you want to do in general, you can analyze directly in the subject's space (most people are doing group analysis, so this does not make sense in general)
On 04/27/2017 08:15 AM, Patrycja Naumczyk wrote: > 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 > <mailto: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 <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
