On 5/5/2022 9:53 PM, krystaly 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 be*
https://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 `('
This is an error because there are parentheses in the file name. Remove
them or escape them.
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.
You have your SUBJECTS_DIR pointing to
/usr/local/freesurfer/7.2.0/subjects, and you don't have write
permission to that folder. Set your SUBJECTS_DIR to a folder where you
have write permissions.
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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