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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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")

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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