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. > -- Jörg Pfannmöller <pfannmo...@uni-greifswald.de> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
