MiDeFace in 7.3.2 does not seem to work #1042
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uptime is a system command. Can you check if it is in your PATH? It is probably in /usr/bin. |
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uptime is being run from fs_time. You can turn off this behavior with
unsetenv FS_TIME_ALLOW
But it will be good to know that uptime is not available on your platform.
On 12/22/2022 2:21 PM, yhuang43 wrote:
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uptime is a system command. Can you check if it is in your PATH? It is
probably in /usr/bin.
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I tried to find also tried to |
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use 'export FS_TIME_ALLOW=0' for bash |
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You can also 'export FSTIME_LOAD=0' to just skip uptime. This is probably better because it will still report the execution time. |
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Ah perfect, this did the trick. |
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I am trying to use the Freesurfer script MiDeFace to anonymize my anatomical data.
I am using docker to have the Freesurfer v7.3.2. containerised.
This is the code to run the container
docker run -it --rm -v <path_to_BIDS_dataset>:/data freesurfer/freesurfer:7.3.2when trying to run this code:
mideface --i /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii --o /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.defaced.nii --odir /data/sub-01/ses-01/anat --no-samseg-fast --niiI get the following output, and I did not find any solution online.
Tue Dec 20 16:00:41 UTC 2022
setenv SUBJECTS_DIR /data
cd /root
/usr/local/freesurfer/bin/mideface --i /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii --o /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.defaced.nii
-rwxrwxr-x. 1 root root 27366 Aug 4 04:51 /usr/local/freesurfer/bin/mideface
freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275
$Id$
Linux 86a9c252ea7d 4.18.0-408.el8.x86_64 #1 SMP Mon Jul 18 17:42:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
pid 377
UseXvfb 0
samseg --i /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii --o /data/sub-01/ses-01/anat/tmpdir.midefacer.377/samseg --threads 1 --block-coordinate-descent --options /usr/local/freesurfer/average/mideface-atlas/samseg-options.json
uptime: Command not found.
upt: Subscript out of range.
ERROR:
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