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Hello Krystally,

Try putting the directory Sub-132 under your userid’s home directory, i.e., /home/developer/Sub-132, and then set SUBJECTS_DIR in the environment to point to it.  With the directory Sub-132 specified on your command line, you could then try,
$ export SUBJECTS_DIR=/home/developer

- R.

On May 5, 2022, at 21:53, krystaly <krystaly@hku.hk> wrote:

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Dear Freesurfer experts,
 
 
Before running the command, I have converted DICOM files into NIFTI files.  I, then, moved the nii files to Desktop at FS.  They are in the folder named “Sub-132”.  However, I got the following errors:
 
developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all
bash: syntax error near unexpected token `('
 
To make another attempt, I tried to process with another T1 image, and I got the following error:
 
developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_T1_COR_5_0.5__250_i00002.nii -all
mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied
cp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directory
cat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/patchdir.txt: No such file or directory.
 
I reckoned that the T1 images could not be processed with only 1 plane.  Would you please kindly advise on merging 3-plane T1 images into one comprehensive T1-weighter image for further processing? Or would you please let me know what went wrong in this case?
 
Thanks.
 
Best regards,
 
Krystal
 
 
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