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/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: fsbuildmailto:fsbuild@contbay.com Sent: Friday, May 6, 2022 11:31 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: krystalymailto:krystaly@hku.hk 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:

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...https://secure-web.cisco.com/1UHVC1FSZYmyuNB9-Imz9busENdngVDz-sSAkkWD-mKGV9WnletKDmDav6XNh4DeufrnDsxlVSaMuIYqWMnp2hLM3OoPum_g7pP6r7ilayKRTXVKkLWOtldS6xNiyHXQfxvgCt2ouIPS3x05icPfPrnunp8pV6-x_Y36h3uUGIUqJG1UNdnKWioAtAuKXqMznQXSN7bza3kVliqHiLrq_py0C20DDvg8QgE1r3G6er-TK6ddpq77V4-sP1ET_Q9B5rvXkUnePAZOS1CrQxQ5HnCUZ2nWU25otZlabWPg6h8kvqC1D4Sdc_e1pI1HYOYRvTWDcoE6ZK3169cipg_2BFg/https%3A%2F%2Fandysbrainbook.readthedocs.io%2Fen%2Flatest%2FFreeSurfer%2FFS_ShortCourse%2FFS_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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1xj1_o_Dxx7BcPTE610em1PQ9XT8fSa1h2dPfddJJ9kOyd5...