External Email - Use Caution

Hi Paul,

Thank you so much for the timely response and the easy-to-follow explanation (and especially for the little tips on naming/spacing, which are helpful for a new coder). I did all these steps and everything worked great - the recon-all is running fine now.

Thank you!

Joanna

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <PWIGHTON@mgh.harvard.edu>
Sent: Thursday, May 5, 2022 1:26 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

Hi Joana,

There are a few things going on here.

First, you should create a subjects directory for FreeSurfer recons and tell FreeSurfer where it is by setting the SUBJECTS_DIR environment variable. You should be able to do that with these 2 commands:

```

mkdir -p /home/developer/guest_shared/fs-subjects

export SUBJECTS_DIR=/home/developer/guest_shared/fs-subjects

```

Next, it looks like you've downloaded the dataset to a folder called `/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/` and the spaces in the folder name are confusing recon-all. Can you rename that directory and remove the spaces? You should be able to do that in the file explorer, but this should also work:

```

mv '/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/' /home/developer/guest_shared/mv-ds000174-1.0.1-Cannabis/

```

You should then be able to run the recon-all command. However, when running recon-all, you might want to rename the subject from 'sub101' to 'sub101-sesBL' (recon-all -s sub101-sesBL) so that you don't confuse it with the follow-up session (ses-FU) in the dataset.

-Paul

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Joanna L Eckhardt <jeckhardt@health.ucsd.edu>
Sent: Thursday, May 5, 2022 3:37 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thank you!

Joanna