Hello freesurfer experts, I am having difficulties using mris_ca_train and mris_ca_label. I am trying to get third party-software to accept a user-defined parcellation in the form of a .gcs file, which I created from sample data using mris_ca_train. I have reproduced the portion of the workflow that is buggy. When I run the software, it calls mris_ca_train, followed by mris_ca_label and mri_annotation2label. On mri_annotation2label, it produces the following output and writes no label files:
[truffles:mridat] (nmr-stable5.1-env) mri_annotation2label --subject nmr00535_FS --hemi lh --annotation icotest --outdir nmr00535_FS/label/regen subject = nmr00535_FS annotation = icotest hemi = lh outdir = nmr00535_FS/label/regen surface = white Reading surface /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/surf/lh.white Loading annotations from /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot reading colortable from annotation file... colortable with 643 entries read (originally /cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/ico3_regenerated_clut_lh.txt) Seg base 0 *max index = -1* The annotation at this point is corrupted and cannot be opened in matlab and shows up empty in tksurfer. The annotation I started with as input to mris_ca_train shows up just fine. The commands i used for mris_ca_train and mris_ca_label are as follows: mris_ca_train -t $TEST_DIR/ico3_clut.txt lh sphere.reg ico3_morph $SUBJECTS $TEST_DIR/lh_test.gcs mris_ca_label nmr00535_FS lh sphere.reg $TEST_DIR/lh_test.gcs $TEST_DIR/nmr00535_FS/label/lh.icotest.annot Can anyone point out where my labels are being clobbered? thanks, R -- Roan LaPlante Athinoula A. Martinos Center for Biomedical Imaging
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