Hi Rebecca,

Thanks for sending the file. But it doesn’t seem that I have the permission to access it.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Rebecca Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Dear Yujing,

Thank you kindly for your support. Please see attached.

Kind regards,

Rebecca

Downloads.zip

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing
Sent: Tuesday, 26 April 2022 8:34 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error

Hi Rebecca,

We would like to understand why those dicom files are not recognized by Freesurfer. If it is possible, can you provide us some of those dicom files to debug?

Thanks.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error

Hi Rebecca,

Thank you for the information.

I'm wondering if you would like to try converting those dicom using dcm2niix to .nii, and then feed .nii to recon-all pipeline.

You can download dcm2niix here:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/rordenlab/dcm2niix

I use the following command to do conversion: dcm2niix -o <output dir> -f "%s_%p" <dicom dir>

Please note that <dicom dir> needs to be specified as last parameter. '-f <>' specifies output file name format - "%s_%p" will have series no + protocol as prefix.

Hope these helps.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.au>
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Hi Yujing,

I guess not. This is the output:

cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ mri_probedicom --i /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256

ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 is not a dicom file or some other problem

Entering IsDICOM (/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)

ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 is not a dicom file or some other problem

I also ran straight to the dicom files themselves, with the same response:

ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 is not a dicom file or some other problem

Entering IsDICOM (/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 as part10

DCM_FILEOPENFAILED

20092 DCM failed to open file: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM (/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

ERROR: /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 is not a dicom file or some other problem

Thank you,

Rebecca

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing
Sent: Friday, 22 April 2022 11:11 PM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: 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.

Confirmed I am running Freesurfer 6.0.
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.
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

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.edu>
Sent: Friday, 22 April 2022 4:19 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: 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.

Can you confirm that you are running Freesurfer 6.0?
>From which directory, did you run recon-all and dcmunpack?
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

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