Dear Freesurfer Experts,
I was able to use mris_ca_train to produce a atlas (.gcs) file with all the labels I am interested in, and I also modified the surface_labels.txt in the freesurfer folder so only the labels I am interested are listed on the txt file. however, when I try to use mris_ca_label to apply the label onto the different brain. The names of each label doesn't transfer, I'd get names like parcellation 20 30 150. Is there anyway to fix this?
sincerely, Andy S
Andy,
Possibly the colortable wasnt saved in the .gcs file. I've attached a couple scripts we use to create our .gcs files. The first, create_aparc_edited_annot, creates a .annot file from your labels. Note that all labels are explicitly listed. Then, the script build_desikan_killiany_gcs creates the .gcs file from the .annot file just created. Both scripts take the colortable file as input. The colortable file is the same format as the surface_labels.txt file, but just contains the labels composing the atlas (probably what you already have created for yourself).
Nick
On Tue, 2009-05-26 at 10:50 -0700, xforever@ucla.edu wrote:
Dear Freesurfer Experts,
I was able to use mris_ca_train to produce a atlas (.gcs) file with all the labels I am interested in, and I also modified the surface_labels.txt in the freesurfer folder so only the labels I am interested are listed on the txt file. however, when I try to use mris_ca_label to apply the label onto the different brain. The names of each label doesn't transfer, I'd get names like parcellation 20 30 150. Is there anyway to fix this?
sincerely, Andy S _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
send us your mris_ca_train command line. It should specify the location of the color lookup table (e.g. surface_labels.txt) to include in the .gcs file, which will then put it into the automated labeling files (.annot) for tksurfer to read.
Bruce On Tue, 26 May 2009 xforever@ucla.edu wrote:
Dear Freesurfer Experts,
I was able to use mris_ca_train to produce a atlas (.gcs) file with all the labels I am interested in, and I also modified the surface_labels.txt in the freesurfer folder so only the labels I am interested are listed on the txt file. however, when I try to use mris_ca_label to apply the label onto the different brain. The names of each label doesn't transfer, I'd get names like parcellation 20 30 150. Is there anyway to fix this?
sincerely, Andy S _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Nick Schmansky -
xforever＠ucla.edu