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: coope...@student.unimelb.edu.au<mailto:coope...@student.unimelb.edu.au> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu<mailto: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
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