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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro Leon <bertocerron@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

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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?