Thanks . Its working now. ___________________________________T_____ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 11 April 2017 16:48 To: Freesurfer support list Subject: Re: [Freesurfer] mris_ca_label giving error CTABfindAnnotation: ct was NULL

when you run mris_ca_train use -t <color table name> and it will embed it in the .gcs file

On Tue, 11 Apr 2017, Das S. wrote:

Hi, I have created a color table, an annot file and a .gcs file( attached with the mail). But when I am trying to execute mris_ca_label with my own .gcs file I am getting the error :

mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh lh.sphere.reg 100307/label/lh.eq40aparc.gcs 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.eq40aparc.gcs... average std = 0.2 using min determinant for regularization = 0.001 0 singular and 185 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory

.....

Before this I have used the below commands, to sucessfully create the .annot and .gcs file:

1. To create .annot file from label files and CTAB file--

mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/MyColorLUT.txt --a eq40aparc --ldir 100307/label/eq_parcellation_label

2. To crate .gcs file from annot file.

mris_ca_train rh 100307/surf/rh.sphere 100307/label/rh.eq40aparc.annot 100307 100307/label/rh.eq40aparc.gcs

I am not be able to understand where is the problem. Any help will be appreciated. Thanks Sarbani

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