Hi Rebecca,

I’m trying to get more information to determine how it core dumped.

1. Can you confirm that you are running Freesurfer 6.0?
2. From which directory, did you run recon-all and dcmunpack?
3. Can you try dcmunpack by passing it full path to dicom directory?

Thanks.

Yujing

-------- Forwarded Message --------

Subject:	[Freesurfer] recon-all error
Date:	Sun, 10 Apr 2022 07:01:30 +1000
From:	cooperr1@student.unimelb.edu.au
Reply-To:	Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
To:	freesurfer@nmr.mgh.harvard.edu

        External Email - Use Caution        

Dear FreeSurfer developers,

I’m attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below.

Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all

Error message:
/Applications/freesurfer_v6/bin/mri_convert: line 3:  8196 Segmentation fault: 11  mri_convert.bin "$@"

The recon-all.log is also attached.

I’ve also explored using dcmunpack and obtain the following result:

Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256

Message:
cat: /tmp/dcmdir-all.89439: No such file or directory

Found 0 unique series:

Patient: Undefined variable.

Do you have any idea what might be the problem?

Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Platform: Mac OS X 10.13.3

Recon-all.log: attached.

With warm regards,

Rebecca Cooper