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Hard to look at the error w/o a core dump file, but I suspect “bus error” is from the VM and not from commands in the recon-all acting differently during your 2nd run..

It reads like you created a shared folder for the VM to use, and set SUBJECTS_DIR to it so the recon-all will write files to the D: drive which I assume has a windows file system (NTFS) and not a linux file system (ext4).

Bus error could be from the VM not being able to do something on the D drive when it needed to.  It’s not going to work by default for something running in the linux VM to create a soft link on a Windows file system.  There are some postings about how to enable this, but it’s a pain, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://stackoverflow.com/questions/50036128/windows-issue-with-symlinks-in-vbox-shared-folders

I would avoid pointing SUBJECTS_DIR to a windows file system for the linux VM to write to.   If you want disk space usage on your C  drive, consider locating the VM on your external D drive (which should also help the VM run faster since it won’t be running from the boot drive).   You can take your existing VM on the C drive and clone it to a new folder/destination on your D drive using the VirtualBox application.  Then you should have 2 instances of the VM.  Test bringing up the one on the D drive and then delete the one on the C drive including all its files.

- R.

On Aug 31, 2022, at 18:32, daedalus39@aol.com wrote:

        External Email - Use Caution        


Hello FreeSurfer Developers,

In an effort to relieve strain on my local C:/ drive, I was testing "export" to an existing shared folder on my SSD drive (D:/)

Guidance came from:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52250.html
export SUBJECTS_DIR=/media/sf_0007_Subjects-FS/subjects

I had tested the FS-7.2 VM on this same image leaving the SUBJECTS_DIR environment variable as default and this MRI was processed and ran to completion without error. 

While certain early portions for FS ran without issue for this 2nd test (shared folder in the VM set up upon installation), the recon-all run exited with errors at the Nu Intensity Correction step. 

Bus error 
Command exited with non-zero status 1 


I don't understand how "mri_binarize" could crash and I'm hoping you can provide some guidance..  

Did I need to use a variation of the command:
mkdir -p /home/developer/guest_shared/sf_0007_Subjects-FS/subjects
(?)

I am running all this on the VM FS_Ubuntu_18_04_06.

Thanks in advance for any insight.

-Randy

PS. I only know enough Linux to get into trouble


-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.2.0
FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjects
MNI_DIR           /usr/local/freesurfer/7.2.0/mni




xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx from recon-all.log xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

#@# Nu Intensity Correction Wed Aug 31 14:19:28 EDT 2022

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 

/usr/bin/bc
/media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mri
/usr/local/freesurfer/7.2.0/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
nIters 2
mri_nu_correct.mni 7.2.0
Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
Wed Aug 31 14:19:28 EDT 2022
tmpdir is ./tmp.mri_nu_correct.mni.6181
cd /media/sf_0007_Subjects-FS/subjects/WBI-FES_S_0862x/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.6181/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_binarize --i ./tmp.mri_nu_correct.mni.6181/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.6181/ones.mgz
Bus error 
Command exited with non-zero status 1
@#@FSTIME  2022:08:31:14:19:28 mri_nu_correct.mni N 9 e 139.45 S 1.50 U 137.65 P 99% M 508172 F 1 R 155334 W 0 c 291 w 1359 I 720 O 0 L 0.91 0.50 0.26
@#@FSLOADPOST 2022:08:31:14:21:48 mri_nu_correct.mni N 9 2.37 1.22 0.56
Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s WBI-FES_S_0862x exited with ERRORS at Wed Aug 31 14:21:48 EDT 2022

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