After spmregister, you can run mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii
# mask out the cortical structures mri_mask pet.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz pet.tal2mm.subc.nii # Concatenate all subjects together mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o all.pet.tal2mm.subc.nii --prune # smooth mri_fwhm --i all.pet.tal2mm.subc.nii --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X --smooth-only --o all.pet.tal2mm.subc.smoothed.nii mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C 2gc0.mtx --glmdir subc.glmdir On 10/19/2016 05:09 PM, John Anderson wrote: > Dear experts, > I ran surface based analysis using PET maps. As the following: > spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh > mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii > subject1/pet/pet_2_T1_register.dat ..... --projfrac 0.5 --out lh.mgh > mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval > lh.sm6.mgh > mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh > --cortex --glmdir lh.glmdir// > then mri_glmfit-sim to correct for multiple comparison. > I want to study the subcortical regions and map it on MNI305. How can > I resume tha analysis for subcortical structures? > Thank you for any help! > Bests, > John > > > _______________________________________________ > 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 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.
