Try it with --fill-ribbon On 09/08/2015 11:01 AM, Hirsch, Gabriella wrote: > Hi all, > > I'm trying to generate an ROI mask from the Freesurfer label > lh.MT.label of a specific subject. I've browsed the documentation and > the archives and it seems the best command to use is mri_label2vol. > However, I can only seem to produce the "outline" of the label, if > that makes sense (as when you load the label on an inflated brain in > tksurfer). > > Is there any way to create a 3D "filled in" ROI in .nii format to then > use in FSL, for instance? I tried playing around with the values in > the --fillthresh and --proj flags but no dice. > > Here is the command I've been using: > > * mri_label2vol --label $SUBJECTS_DIR/*MBZ_07102015*/label/lh.MT.label > --label$SUBJECTS_DIR/*MBZ_07102015/label/lh.MT.label --temp > $*SUBJECTS_DIR/*MBZ_07102015/mri/T1.mgz --reg* > $SUBJECTS_DIR/*MBZ_07102015/stats/register.dat* *--fillthresh 0 --o* > $*SUBJECTS_DIR**/MBZ_07102015/new_lh.MT.nii.gz > Any suggestions would be greatly appreciated! > > Thanks, > Gabriella > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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