That is good suggestion. ‘recon-all’ should check if any processing directive
presents before proceeding to process the data.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ben Wagner
Sent: Thursday, March 6, 2025 2:05 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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/BugReporting<https://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>
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
