On May 6, 2022, at 04:17, krystaly <krystaly@hku.hk> wrote:

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Dear R.,

 

Thanks for your reply.

 

My apologies if I did not totally get your point – I moved the Sub-132 folder to Home directory and typed in the command as you suggested.  However, I still got the error as follows:

 

developer@developer-VirtualBox:~$ export SUBJECTS_DIR=/home/developer

developer@developer-VirtualBox:~$ 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 `('

developer@developer-VirtualBox:~$ ls

Desktop    ExternalHD.txt  license.txt  Pictures  Templates

Documents  fsl_507         matlab       Public    Videos

Downloads  guest_shared    Music        Sub-132

developer@developer-VirtualBox:~$ cd Sub-132

developer@developer-VirtualBox:~/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 `('

developer@developer-VirtualBox:~/Sub-132$

 

Would you please kindly advise?

 

Thank you so much!

 

Best regards,

 

Krystal

 

 

From: fsbuild
Sent: Friday, May 6, 2022 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: krystaly
Subject: Re: [Freesurfer] Recon-all

 

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,

 

I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as demonstrated on the website (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html).

 

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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