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
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?