External Email - Use Caution
Dear Freesurfer experts, I am using "mris_divide_parcellation" in order to increase the region numbers of Freesurfer parcellation output using "recon-all". e.g i have a 200-region parcellation.Now i wanna use "mris_ca_train" and this .annot file as an input to create an atlas file(.gcs). The code i run and the results on the terminal are : $ mris_ca_train lh sphere.reg LDestrieux200 test1 $SUBJECTS_DIR/test1/label/lh.Destrieux200.gcs computing means for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 4210 classifier means computed, 1.6/vertex, 0.5 priors/vertex computing covariances for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 75009 holes filled in class prior array 0 holes filled in gcsan array writing classifier array to /home/user/Desktop/Maedeh/test1/label/lh.Destrieux200.gcs... classifier array training took 0 minutes and 4 seconds.
the problem is that when i use "lh.Destrieux200.gcs" and "mris_ca_label" to create an annotation file, the result i have is kinda awful !! and when i check it by tksurfer , the parcellation is not complete and i just see few regions...i dunno where i am making a mistake. the code and the results on terminal are : mris_ca_label test1 lh sphere.reg lh.Destrieux200.gcs $SUBJECTS_DIR/test1/label/lh.myDestrieux200.annot $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from lh.Destrieux200.gcs... average std = 0.2 using min determinant for regularization = 0.000 0 singular and 570 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 479 changed, 114679 examined... 001: 18 changed, 2844 examined... 002: 1 changed, 89 examined... 003: 0 changed, 5 examined... 000: 241 total segments, 38 labels (248 vertices) changed 001: 203 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) writing output to /home/user/Desktop/Maedeh/test1/label/lh.myDestrieux200.annot... classification took 0 minutes and 3 seconds.
I would be grateful if u could help me. Cheers, Maedeh,