Re: [Freesurfer] recon-all error

Hi Rebecca,

I’m wondering if the dicom files are being recognized.

Can you run the following command with some dicom files in the directory? mri_probedicom --i <your_dicom_file> --d filetype

(Replace <your_dicom_file> with full path to dicom file.)

Thanks.

Yujing

From: cooperr1@student.unimelb.edu.au cooperr1@student.unimelb.edu.au Sent: Friday, April 22, 2022 1:34 AM To: Huang, Yujing YHUANG43@mgh.harvard.edu; 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon-all error

External Email - Use Caution Dear Yujing,

Thank you for your reply.

1. Confirmed I am running Freesurfer 6.0. 2. I am running both commands from within the individual subject directory (ID=1003156). The parent folder contains several folders all labelled with different subject IDs, and within each contains the dicom directories. 3. I attempted this and received the error:

/Applications/freesurfer_v6/bin/dcmunpack -src /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/

-rwxr-xr-x 1 chesterk admin 23759 Jun 14 2018 /Applications/freesurfer_v6/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Fri Apr 22 15:32:30 AEST 2022 Fri Apr 22 15:32:30 AEST 2022 Found 114 total files. Interrogating each and every one of them. Be patient. If you have collected the data in the Martinos center, this will run faster if you kill this job and re-run with -martinos Except, with changes in the file naming (Oct 2012), this does not work. cat: /tmp/dcmdir-all.23294: No such file or directory Found 0 unique series: Patient: Undefined variable.

With thanks, Rebecca

From: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Friday, 22 April 2022 4:19 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au Subject: RE: [Freesurfer] recon-all error

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.aumailto:cooperr1@student.unimelb.edu.au Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edumailto: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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