Thanks Joanna, that's great to hear!

-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 8:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

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"

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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/BugReportinghttps://secure-web.cisco.com/171g7W4aWq3g90gDYi_bDLIcS8Y5d6ZDSv8P1BtEB0c8Ly1DMxcJKeele5KmRxWCr7JKNdg8_cR8pzKb88y59RAmrRPw7dGEJQTvCtv4h0x6N1ZiilaHpEk4LMcmAPsyeY-iPJLIE6RyQ3L5RbhWKRItLqD1FEGK2nhdzOvL5G4hexVN_J_6lFzXepUiL7tld08Z1rUJ4_aMPiQqe9Ek7cHaP8G3mPzorvHiqhDwBwUPyJr6lAhVVDlr-fHJIawFUzNoftzSKnLT_haniNl_I3V4rplErUmApmK5NdpbX6UOL5JiFkXqqCd9RHPaUxzfW/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting%26d%3DDwQFAg%26c%3D-35OiAkTchMrZOngvJPOeA%26r%3DVOzaW5NbE-ma6Pc9pAKE20dZgxgmYGpxFACLfTD0LGQ%26m%3DW5PopnSfVtKWxkgSaUNs7m5Lv8OXa-7tySQEG8PF4v0P4zG1F4pLbFo-tiG-jK4z%26s%3Dlhc8hKnWtmbg0fMq6WvmQp3cLJHpxoLkY8ClfO6CcsE%26e%3D

Thank you! Joanna