Just subcortical. BTW, going to 1mm will probably create very large files. doug
On 11/28/2012 03:52 AM, Jörg Pfannmöller wrote: > A last question to this topic. Does the resolution of the MNI305 brain > affected the surface based analysis or is it exclusively affecting the > subcortical analysis? > > On Tue, 27 Nov 2012 13:30:04 -0500 > Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > >> Note that each of those set commands should be a single line. The file >> to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess >> >> doug >> >> >> On 11/27/2012 01:23 PM, Douglas N Greve wrote: >>> Yep, that's a bug. I've fixed it in my version. To fix it in yours, do >>> the following two steps: >>> >>> Step 1: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz >>> cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri >>> >>> Step 2: In rawfunc2tal-sess, change: >>> >>> set subcortmask = >>> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz >>> >>> To >>> >>> if($res == 2) then >>> set subcortmask = >>> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz >>> else >>> set subcortmask = >>> $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz >>> endif >>> >>> doug >>> >>> On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote: >>>> Hi, >>>> >>>> if I apply the following command: >>>> >>>> preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh >>>> -mni305-1mm -fwhm 0 -per-run -nosmooth -force >>>> >>>> The preprocessing runs into trouble at the following point >>>> >>>> mri_vol2vol done >>>> >>>> mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii >>>> /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz >>>> /...path.../bold/001/masks/brain.mni305.1mm.nii >>>> freadFloat: fread failed >>>> ERROR: dimension mismatch between source and mask >>>> >>>> As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which >>>> results in the dimension mismatch. How can I get rid of this problem? >>>> >>>> Cheers Joerg >>>> _______________________________________________ >>>> 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: 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. >> > -- 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: 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
