Dear FreeSurfer Developer, I have created my own atlas file and from the atlas file created the annot file. When I am trying to load my annot file on the sphere surface and view in tksurfer, I am getting below error:
7607 vertices did not have an annotation!
I have the below steps in sequence:
1. I am creating my label files from matlab and keeping them in a folder.
2. From the labelled files I am creating the annot file using the below command: mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/MyColorLUTnew.txt --a eqnew40aparc --ldir 100307/label/eq_parcellation_label/
3. When I am loading this lh.eqnew40aparc.annot file on sphere surface in tksurfer , it showing me all labels perfectly. tksurfer 100307 lh sphere
4. Then I am creating the .gcs file from the annot file using below command. The gcs files is being created without any error . mris_ca_train -t 100307/label/eq_parcellation_label/MyColorLUT.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.left40aparc.annot 100307 100307/label/lh.reg40aparc.gcs
5. Then I am creating the .annot file using the my created atlas file using the below command: mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.eqnew40aparc.gcs 100307/label/lh.aparc.annot using 100307/mri/aseg.presurf.mgz aseg volume to correct midline $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 100307/label/lh.eqnew40aparc.gcs... reading color table from GCSA file.... average std = 0.2 using min determinant for regularization = 0.001 0 singular and 194 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 572 labels changed using aseg relabeling using gibbs priors... 000: 284 changed, 133181 examined... 001: 8 changed, 1741 examined... 002: 0 changed, 37 examined... 2 labels changed using aseg 000: 67 total segments, 24 labels (284 vertices) changed 001: 44 total segments, 1 labels (2 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to 100307/label/lh.aparc.annot... classification took 0 minutes and 6 seconds. koushik@koushik-DQ77MK:~/Parcellation$
6. Now when I am trying to see this file in tksurfer loading as annot file on sphere surface I can see a big patch of gray color and showing me the message : 7607 vertices did not have an annotation! [X]
I am attaching the .annot file , .gcs file and colortable .Plase help me to understand where the thing is going wrong,Any help will be much appreciated. Thanks & regards Sarbani