can you send the recon-all.log file?
On 6/26/2025 4:42 AM, 岳昊 wrote:
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Dear FreeSurfer Developers,
I am a neuroscience student currently working on analyzing ASL MRI data using ASLPrep. I am encountering difficulties running recon-all during the preprocessing pipeline.
Specifically, I am running the command recon-all, and the exact error message displayed is
Cmdline:
recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 8 -subjid sub-OAS30001 -sd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer
Stdout:
ERROR: Flag -rh-only unrecognized.
I encountered an issue similar to one reported on GitHub, suggesting a FreeSurfer version incompatibility. Attempts to resolve this by using FreeSurfer version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c and freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b did not resolve the original issue. Upgrading to FreeSurfer version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 resulted in a complete failure of ASLPrep.
For your reference, the following information may be relevant:
1).FreeSurfer Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c, and freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b and freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460.
2).Platform: Red Hat Enterprise Linux 8.5 (Ootpa)
3).uname -a: Linux cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux
4).recon-all.log and the crash file: Please find those files attached to this email.
Any guidance you could provide in resolving this issue would be greatly appreciated. Thank you for your time and assistance.
Sincerely,
Hao Yue
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