There is a space in your path
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.
Rename the directory name and try again.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of ???
Sent: Sunday, March 31, 2024 11:18 PM
To: FreeSurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all mri_convert error: extra argument
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")
External Email - Use Caution
Hello FreeSurfer Developers,
I'm writing to ask for help while using "recon-all" command.
I have converted some dcm format files to to nii format. Then I ran the
command "recon-all -s maoyipeng -i first_sT1W_3D_TFE_tra_MR350895.nii -all", an
error appeared:
mri_convert /home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe
similar/first_sT1W_3D_TFE_tra_MR350895.nii
/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz
mri_convert: extra argument
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")
type mri_convert -u for usage
Command exited with non-zero status 1
@#@FSTIME 2024:04:01:09:09:04 mri_convert N 3 e 0.00 S 0.00 U 0.00 P
100% M 5972 F 0 R 236 W 0 c 0 w 1 I 0 O 0 L 0.43 0.24 0.19
@#@FSLOADPOST 2024:04:01:09:09:04 mri_convert N 3 0.43 0.24 0.19
Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s maoyipeng exited with ERRORS at Mon Apr 1 09:09:04 HKT 2024
I've searched the list and didn't find a similar question. I'm a bit new to
FreeSurfer, so I am unsure how to resolve this issue. I've attached the
recon-all.log if that might help.
1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
2) uname -a: Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
3) recon-all.log: see attached
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