External Email - Use Caution
Hi FreeSurfer Team,
I am trying to run Recon-all on the cannabis test data on the freesurfer
tutorial (I am running Ubuntu 18 VM on Windows os).
When I try to use the Recon-all command, I get the error "Command exited with
non-zero status" and "recon-all -s sub101 exited with ERRORS." Can you help me
solve this?
I am completely new to coding/Ubuntu so I am also confused about the
SUBJECTS_DIR. Where can I find that folder? I do not see
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.
Also, if there is a better way to export and present my code to you other than
copy-pasting it as I have done below, please let me know so I can do that with
future emails.
developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101
mri_convert /home/developer/guest_shared/mv ds000174-1.0.1
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz
mri_convert /home/developer/guest_shared/mv ds000174-1.0.1
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz
mri_convert: extra arguments
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)
type mri_convert -u for usage
Command exited with non-zero status 1
@#@FSTIME 2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub101 exited with ERRORS at Thu May 5 15:24:40 EDT 2022
For more details, see the log file
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see
http://secure-web.cisco.com/1nsoXu7DCJVVepnD_TI4lsupkcqto3lUNXVTynw-dkWgX0jgK5OMP6_Zvr1ZiIw5bdjvsH7QIZbXzwlVuvV8YaYPH31dXZld0PLKJQ6n6zVlT1vUWUcUvBjU9xD9Ofzw8OBKU4eRC_2DIyDBkLIBwF4vsHAAyJZ-hBJL7quyFxlQJ0salWFI5a5qUmD_AkXgyYHjsrbT5WlaGtqn-I72qhlbZm7rYYNqy2AO94040Acgj_3O1wejt1NmgePGUIMn08354kq_0lTEmwZFZX3GhybUyvRiTJq2YRAfWTZBVP9vbm7ve54riG7fhPUzP37cI/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
Thank you!
Joanna
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
