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Hello Freesurfer devs,
I'm trying to test Freesurfer 8.0 but I am encountering an error importing the
T1 image. In previous versions I'd use this command "recon-all -s SUBJECT -i
T1.nii" to import the data and then run "recon-all -s SUBJECT -qcache -all" to
process. Under 8.0, when I run the import command I'm getting the error below,
but basically the orig.mgz file is never created. It has been hinted in the
help the processing directive was required in the past, has it finally become
so?
Thank,
Ben
mri_synthstrip --threads 1 -i
/endosome/archive/shared/fs8_trial/SUBJECT/mri/orig.mgz -o
/endosome/archive/shared/fs8_trial/SUBJECT/mri/synthstrip.mgz
Configuring model on the CPU
Running SynthStrip model version 1
Traceback (most recent call last):
File
"/project/shared/ANSIR/software/freesurfer/8.0.0/python/scripts/mri_synthstrip",
line 261, in <module>
image = sf.load_volume(args.image)
File
"/project/shared/ANSIR/software/freesurfer/8.0.0/python/lib/python3.8/site-packages/surfa/io/framed.py",
line 41, in load_volume
return load_framed_array(filename=filename, atype=Volume, fmt=fmt)
File
"/project/shared/ANSIR/software/freesurfer/8.0.0/python/lib/python3.8/site-packages/surfa/io/framed.py",
line 119, in load_framed_array
check_file_readability(filename)
File
"/project/shared/ANSIR/software/freesurfer/8.0.0/python/lib/python3.8/site-packages/surfa/io/utils.py",
line 24, in check_file_readability
raise FileNotFoundError(f'{filename} is not a file')
FileNotFoundError: /endosome/archive/shared/fs8_trial/SUBJECT/mri/orig.mgz is
not a file
@#@FSTIME 2025:03:05:12:07:38 mri_synthstrip N 6 e 3.49 S 1.10 U 2.26 P 96% M
244216 F 0 R 84830 W 0 c 133 w 8576 I 0 O 0 L 4.08 4.28 4.24
@#@FSLOADPOST 2025:03:05:12:07:41 mri_synthstrip N 6 3.83 4.22 4.23
Linux Nucleus173 3.10.0-1160.88.1.el7.x86_64 #1 SMP Sat Feb 18 13:27:00 UTC
2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SUBJECT exited with ERRORS at Wed Mar 5 12:07:41 CST 2025
For more details, see the log file
/endosome/archive/shared/fs8_trial/SUBJECT/scripts/recon-all.log
To report a problem, see
http://secure-web.cisco.com/1ToDWv36nchbVd9vy63S26kW5fcy6Fqjicd_-OqrsrdXkotZDKsrUQrT80jFx2NawWN67KmBGLkH6M9cfD3vyI1JRLiJfXYTAXgL_V1VqLJGWKVsOBlTWhi9RVJXHN5hb8VbYCcJ0el1iaC2rlafwrYtkRQ-Trxzxpj53-zh2O9rxUjRJhsvYgH0g2z_WGdVBSlG-xsPaikGepoaRC_MFJuEZTDGAz6GXiYbZk-FCsHgBYdXE4e2AR68Xd4GjSs-jIT50xeP9HxN2gOTjSo_TGg7CFXBqTovIxI5rVrrSA81DT3zhrDVFwCPkbKK4Qk4KYaAk_FYfnDB9DAyeSzIwcg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
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