External Email - Use Caution
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.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B