RE: [Freesurfer] RE: regional cortical thickness
Hi, I sent an e-mail few days ago asking for the direction to create a medial wall label by mapping all the labels in aparc.a2005 to label files with mri_annotation2label to mask the non cortical regions on the thickness map. Can someone help me? Thanks Valentina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Total Cerebral Volume
Hello everyone,Can someone please point out where freesurfer outputs the total cerebral volume (white + gray).Thanks,Anil. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tables for mri_annotation2label
Hi, When running mri_annotation2label, what is the correct table to give the --table option for ?h.aparc.annot ? $FREESURFER_HOME/Simple_surface_labels2005.txt is the table for ?h.aparc.a2005s.annot, right? Thanks! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Total Cerebral Volume
Hi Anil, you can just add up the relevant classes in the aseg.stats file Bruce On Thu, 26 Oct 2006, Anil Roy wrote: Hello everyone, Can someone please point out where freesurfer outputs the total cerebral volume (white + gray). Thanks, Anil. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tables for mri_annotation2label (fwd)
In the same vein of mri_annotation2label: When I ran mri_annotation2label --subject subj25_bay2 --hemi rh --labelbase $SUBJECTS_DIR/subj25_bay2/label/aparc-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt (where $SUBJECTS_DIR is ~dahlia/structurals/) on mirabai in the nmr-std-env, 11 of 35 labels were created, and for the rest it said 'skipping' (e.g. the snippet below). How can I get all the labels to be created from the annotation file? Thanks! Dahlia. 0 0 --- skipping 1 0 --- skipping 2 0 --- skipping 3 0 --- skipping 4 0 --- skipping 5 0 --- skipping 6 2479 /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-006.label LabelWrite: saving to /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-006.label 7 0 --- skipping 8 6499 /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-008.label LabelWrite: saving to /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-008.label 9 0 --- skipping 10 0 --- skipping -- Forwarded message -- Date: Thu, 26 Oct 2006 16:13:05 -0400 (EDT) From: Dahlia Sharon <[EMAIL PROTECTED]> To: freesurfer@nmr.mgh.harvard.edu Subject: tables for mri_annotation2label Hi, When running mri_annotation2label, what is the correct table to give the --table option for ?h.aparc.annot ? $FREESURFER_HOME/Simple_surface_labels2005.txt is the table for ?h.aparc.a2005s.annot, right? Thanks! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tables for mri_annotation2label (fwd)
Hi Dahlia, I'm not sure if this will work, but try adding --annotation aparc.a2005s This tells mri_annotation2label to use the 2005 labels. This flag seems to be missing from the fswiki but is mentioned in mri_annotation2label --help I got 78 of 82 labels this way, the other four say --- skipping Mike Dahlia Sharon wrote: In the same vein of mri_annotation2label: When I ran mri_annotation2label --subject subj25_bay2 --hemi rh --labelbase $SUBJECTS_DIR/subj25_bay2/label/aparc-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt (where $SUBJECTS_DIR is ~dahlia/structurals/) on mirabai in the nmr-std-env, 11 of 35 labels were created, and for the rest it said 'skipping' (e.g. the snippet below). How can I get all the labels to be created from the annotation file? Thanks! Dahlia. 0 0 --- skipping 1 0 --- skipping 2 0 --- skipping 3 0 --- skipping 4 0 --- skipping 5 0 --- skipping 6 2479 /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-006.label LabelWrite: saving to /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-006.label 7 0 --- skipping 8 6499 /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-008.label LabelWrite: saving to /homes/6/dahlia/structurals//subj25_bay2/label/aparc-rh-008.label 9 0 --- skipping 10 0 --- skipping -- Forwarded message -- Date: Thu, 26 Oct 2006 16:13:05 -0400 (EDT) From: Dahlia Sharon <[EMAIL PROTECTED]> To: freesurfer@nmr.mgh.harvard.edu Subject: tables for mri_annotation2label Hi, When running mri_annotation2label, what is the correct table to give the --table option for ?h.aparc.annot ? $FREESURFER_HOME/Simple_surface_labels2005.txt is the table for ?h.aparc.a2005s.annot, right? Thanks! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
