Hi Yujing,

  I’ve been running “recon-all -s SUBJECT -i T1.nii” without any processing flags to import subjects since at least 5.3 (around 2013).  Somewhere back then it was a recommended pattern even if the tsch usage verbiage from that version calls it required.  Yes I checked.  So, this brings me back to my original question: “It has been hinted in the help the processing directive was required in the past, has it finally become so?”  If it is to be REQUIRED, why is there no initial check before running through 1600 lines of code before failing?

 

Ben

 

 

Processing directive is always required by recon-all. If you would like to process the whole pipeline, use ‘-all’.

 

Yujing

 

 

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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

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