Hi Rachel,

Can you check if you have access to the input files?

  ls -l /usr/home/developer/desktop/TIWI.nii

  ls -l /usr/home/developer/desktop/T2_Flair.nii

Can you attach recon-all.log?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Rachel Wagner
Sent: Friday, February 3, 2023 10:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Directory not set properly?

        External Email - Use Caution        

Hello,

I am trying to run recon-all on my data and am encountering the following issue:

developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i /usr/home/developer/desktop/TIWI.nii -T2 /usr/home/developer/desktop/T2_Flair.nii -T2pial -all

ERROR: cannot find /usr/home/developer/desktop/TIWI.nii

Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 3T00300 exited with ERRORS at Fri Feb  3 10:49:02 EST 2023

For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i sample-001.mgz

ERROR: cannot find sample-001.mgz

Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 3T00300 exited with ERRORS at Fri Feb  3 10:52:53 EST 2023

For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

developer@developer-VirtualBox:~/freesurfer$

Is it that my path is not set correctly?

Thank you!

Rachel Wagner