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Dear,
I'm attempting to execute the recon-all command on the recently released FS
8.1.0 version, however I get an error that I was not getting in prior
versions (6.0 and 7.4.1).
Command:
*recon-all -subjid FREESURFER -sd "/OUTPUT" -i "/INPUT/DATA
input_t1/003MSVISMPRAGE_02.nii.gz" -all *
Output Log:
Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura
-fix-ga -fix-acj -synthstrip -synthseg -synthmorph
fs-check-version --s FREESURFER --o /tmp/tmp.HYwr24
Thu Jul 24 09:29:43 AM UTC 2025
setenv SUBJECTS_DIR /OUTPUT
/usr/local/freesurfer/8.1.0/bin/fs-check-version --s FREESURFER --o
/tmp/tmp.HYwr24
-rwxr-xr-x 1 root root 18565 Jul 19 00:36
/usr/local/freesurfer/8.1.0/bin/fs-check-version
freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed
$Id$
Linux 83857eca32d0 6.8.0-1021-gcp #23~22.04.1-Ubuntu SMP Thu Jan 16
02:17:57 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
pid 126
Current FS Version freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed
Subject does not have a bstampfile, copying
/usr/local/freesurfer/8.1.0/build-stamp.txt
Subject FS Version: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /OUTPUT
Actual FREESURFER_HOME /usr/local/freesurfer/8.1.0
Linux 83857eca32d0 6.8.0-1021-gcp #23~22.04.1-Ubuntu SMP Thu Jan 16
02:17:57 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
/OUTPUT/FREESURFER
mri_convert /INPUT/DATA/input_t1/003MSVISMPRAGE_02.nii.gz
/OUTPUT/FREESURFER/mri/orig/001.mgz
mri_convert /INPUT/DATA/input_t1/003MSVISMPRAGE_02.nii.gz
/OUTPUT/FREESURFER/mri/orig/001.mgz
INFO: using NIfTI-1 sform (sform_code=1)
reading from /INPUT/DATA/input_t1/003MSVISMPRAGE_02.nii.gz...
TR=1970.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0348693, -0.999392, 0)
j_ras = (-0.0330512, -0.00115315, 0.999453)
k_ras = (0.998845, 0.0348502, 0.0330713)
writing to /OUTPUT/FREESURFER/mri/orig/001.mgz...
#--------------------------------------------
*#@# MotionCor Thu Jul 24 09:29:52 AM UTC 2025Found 1
runs/OUTPUT/FREESURFER/mri/orig/001.mgzChecking for (invalid) multi-frame
inputs.../usr/local/freesurfer/8.1.0/bin/UpdateNeeded: line 14: syntax
error near unexpected token
`('/usr/local/freesurfer/8.1.0/bin/UpdateNeeded: line 14: `set Sources =
($argv);'if: Expression Syntax.*
More info:
1) FreeSurfer version:
*freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed*
2) Platform:
Distributor ID: Ubuntu
Description: *Ubuntu 22.04.5 LTS*
Release: 22.04
Codename: jammy
3) uname -a: *Linux eec78b7407cc 6.8.0-60-generic #63~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linu*
Note, I have the 6.0 and the 7.4.1 on the same environment and executed
their recon-all on the same data and they do work.
Best
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