External Email - Use Caution

Sorry if I did not see it before, but parentheses are one of several special characters in the linux/unix shell.  So either don’t use them in file names, or you can try escaping them by preceeding each instance with a backslash so they are interpreted literally, Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all- or you could try putting the entire file name in quotes, "Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all” - R.

On May 6, 2022, at 04:17, krystaly <krystaly@hku.hk> wrote:        External Email - Use Caution        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/developerdeveloper@developer-VirtualBox:~$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -allbash: syntax error near unexpected token `('developer@developer-VirtualBox:~$ lsDesktop    ExternalHD.txt  license.txt  Pictures  TemplatesDocuments  fsl_507         matlab       Public    VideosDownloads  guest_shared    Music        Sub-132developer@developer-VirtualBox:~$ cd Sub-132developer@developer-VirtualBox:~/Sub-132$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -allbash: syntax error near unexpected token `('developer@developer-VirtualBox:~/Sub-132$ Would you please kindly advise? Thank you so much! Best regards, Krystal  From: fsbuildSent: Friday, May 6, 2022 11:31 AMTo: freesurfer@nmr.mgh.harvard.eduCc: krystalySubject: 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:        External Email - Use Caution        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... 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 -allbash: 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 -allmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedmkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission deniedcp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directorycat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directoryINFO: FreeSurfer build stamps do not matchSubject 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  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B