You can use mri_binarize to replace the CC values with WM values, eg
mri_binarize --i aseg.mgz --replace 251 2 --replace 252 2 ... --o aseg.nocc.mgz If your version of mri_binarize does suppor the --replace option, you can get this versoin https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize On 01/17/2017 05:37 PM, Bharadwaj, Pradyumna - (prad) wrote: > > Hi, > > > I've been trying to create WM lobes using the following steps: > > > 1) mri_annotation2label --lobesStrict > > 2) Outputting the labels from step 1, & creating a simpler annotation > without limbic and insular lobes > > 3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub > --annot Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 > --rip-unknown > > > However, as the corpus callosum is not labelled as wm, it is not > included in any WM lobe. > > > Is there any workaround to assigning the corpus callosum to the > different WM lobes or do I have to manually > edit aseg.mgz to change the corpus callosum's value to match that of WM ? > > > > Thanks, > > -Prad > > > > > _______________________________________________ > 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.
