That is good suggestion. ‘recon-all’ should check if any processing directive presents before proceeding to process the data.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ben Wagner Sent: Friday, March 7, 2025 10:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 8.0 without processing directives

External Email - Use Caution 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

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Thursday, March 6, 2025 3:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer 8.0 without processing directives

Processing directive is always required by recon-all. If you would like to process the whole pipeline, use ‘-all’. Yujing From: freesurfer-bounces@ nmr. mgh. harvard. edu <freesurfer-bounces@ nmr. mgh. harvard. edu> On Behalf Of Ben

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

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ben Wagner Sent: Thursday, March 6, 2025 2:05 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer 8.0 without processing directives

External Email - Use Caution 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttps://secure-web.cisco.com/1a2LIo1N11TXHmMLa6zpCXLp01UwnlPLLHahV8AX0tip0ngG6H8YEwMEc_0yl3czgjBYlW2lrzgqtF1zUBuMf_oIKz_Xw8aseLE7xaKYB1NTdrN3KVAuY3hqDMRF0e6pnkMtSw2LnPtv7RJtHHXdJpqs37to2qtFNOnplgm9Q4tfVdnP7xQP9TlXQrGFldmyh3mZqm2lT4IXjtoYTMe4Dz9eMccLz9CmMiQy6x1mSCLx_JtYNmiVRC69o-erQ166ChxvFK2BaIPIasyvlvuynEXXsjdZ3FjS0T6ENjWpYNZfMvyvhTH7t45ttYvB2HGGAom2WRH-SaDcyIoyS-Cx1uA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F1ToDWv36nchbVd9vy63S26kW5fcy6Fqjicd_-OqrsrdXkotZDKsrUQrT80jFx2NawWN67KmBGLkH6M9cfD3vyI1JRLiJfXYTAXgL_V1VqLJGWKVsOBlTWhi9RVJXHN5hb8VbYCcJ0el1iaC2rlafwrYtkRQ-Trxzxpj53-zh2O9rxUjRJhsvYgH0g2z_WGdVBSlG-xsPaikGepoaRC_MFJuEZTDGAz6GXiYbZk-FCsHgBYdXE4e2AR68Xd4GjSs-jIT50xeP9HxN2gOTjSo_TGg7CFXBqTovIxI5rVrrSA81DT3zhrDVFwCPkbKK4Qk4KYaAk_FYfnDB9DAyeSzIwcg%2Fhttp%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FBugReporting__%3BJSUlJSU%21%21MznTZTSvDXGV0Co%21EeyKoF9NvFbl1n4_bRNImfinaNvwhFVtNV3bduj2LcdIANm6zSc6UTaiMihtX0o1eOUXPHwynwGy-lgcMCeA7jlDYr0TNf4AQps%24

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