If the output directory is missing seg.mgz, then samseg failed. You’ll have to
send us the log or some sort of information about the error for us to debug
this.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro Leon
<bertocer...@gmail.com>
Date: Friday, May 7, 2021 at 6:49 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error in SAMSEG preprocessing
External Email - Use Caution
Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the
following command:
run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii'
'/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion
--lesion-mask-pattern 0 1 --output '/home/neuroimage/fsl/vascular/1002/'
The output files were:
* cost.txt
* priors-testing.mgz
* samseg.talairach.lta
* template.lta
* template_coregistered.mgz
* template_transforms.mat
However I don't find any file with the white matter lesions segmented or a stat
file. I would send you the terminal outputs but is too extensive. Would you
help me?
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