It looks like you have a space between “/usr/local/freesurfer/subjects/1268”  and “/label/lh.BN_Atlas.annot”

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ???
Sent: Saturday, October 22, 2022 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_ca_label -l can not generate lh.BN_Atlas.annot

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Hi,
 
When I used "mris_ca_label -l /usr/local/freesurfer/subjects/1268/label/lh.cortex.label 1268 lh /usr/local/freesurfer/subjects/1268/surf/lh.sphere.reg /usr/local/freesurfer/subjects/lh.BN_Atlas.gcs /usr/local/freesurfer/subjects/1268 /label/lh.BN_Atlas.annot"
 
Should this command generate a file “lh.BN_Atlas.annot” in 1268/label? But I can not find this file.
 
7.2.0
  7.2.0
reading atlas from /usr/local/freesurfer/subjects/lh.BN_Atlas.gcs...
reading color table from GCSA file....
average std = 0.5 3.7   using min determinant for regularization = 0.000
0 singular and 619 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
relabeling using gibbs priors...
mris_ca_label supposed to be reproducible but seed not set
000:   6034 changed, 128292 examined...
001:   1428 changed, 24227 examined...
002:    337 changed, 7920 examined...
003:    110 changed, 2057 examined...
004:     43 changed, 677 examined...
005:     17 changed, 253 examined...
006:      3 changed, 89 examined...
007:      0 changed, 20 examined...
000: 232 total segments, 126 labels (607 vertices) changed
001: 112 total segments, 6 labels (7 vertices) changed
002: 106 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 13 changed)
rationalizing unknown annotations with cortex label
0 vertices marked for relabeling...
0 labels changed in reclassification.
writing output to /usr/local/freesurfer/subjects/1268...
classification took 0 minutes and 12 seconds.