Hi Douglas, thanks for the tip - as a new FS user I didn't mastered tkmedit yet, so it's good to know that this viewer supports MNI->orig transformation automatically.
I understand it's unusual to perform a single subject fMRI in freesurfer. It's just that we came across a very interesting case study of pure alexia, in which presenting fMRI results in patient space is crucial for further interpretation. I thought of re-runing the analyses in subject space (as You suggested), and probably will end up doing so. Just for the record and expanding my FS skills, I would very much liked to know - where is my mistake in the process of transforming the 'sig.nii.gz' volumes from MNI to orig space. I suppose that's an issue I may came across in future as well (even if with different files/spaces). So - any help in that matter is still very much appreciated! And also, even though not designed for the purpose of case studies, I have to admit - Freesurfer is so incredible! I processed this very same subject through SPM's fMRI stream, and didn't got even partly as conclusive and precise statistical maps. I've become a huge fan of surface-based analyses :) You're doing amazing job with developing this software! Best regards, Patrycja 2017-04-27 17:14 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > 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:freesur...@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 >
_______________________________________________ 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.
