Sample the raw TAC data onto the surface (and not the BPs), then smooth on the surface, then run the mrtm2 with all the same arguments except use the surface data as the input (--y) instead of the ROI data.
On 08/23/2016 05:13 PM, Jonathan DuBois wrote: > Hi, > > I’m trying to use the PETsurfer Pipeline to perform BP analysis, but > I’m not sure at which point in the pipeline to sample the data to the > surface and what registration to use? > > I tried running the pipeline using dynamic kinetic modeling as > described here: http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, > and then used the following command to try and sample the BP map the > surface: > mri_vol2surf --hemi lh --projfrac .5 --out_type mgh --cortex --mov > mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o lh.bp_pf5.mgh > > But got the following error: > ERROR: source volume is neither source nor target of the registration > > I also tried sampling the mrtm2/bp.nii.gz to the orig.mgz volume space > and then to the surface using: > mri_vol2vol --mov mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o > mrtm2/bp_2anat.nii.gz --targ $SUBJECTS_DIR/subject1/mri/orig.mgz; > mri_vol2surf --hemi lh --projfrac .5 --out_type mgh --cortex --mov > mrtm2/bp_2anat.nii.gz --regheader subject1 --o lh.bp_pf5.mgh > > This worked, although the surface file did not have any values… > > Could you please let me know what is the best way to sample the data > to the surface, and if it should be down prior to mri_glmfit or after. > > Thanks > Jonathan > > > > _______________________________________________ > 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.
