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: fsbuild<mailto:fsbu...@contbay.com>
Sent: Friday, May 6, 2022 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: krystaly<mailto:kryst...@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 <kryst...@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_03_ReconAll.html<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
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