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
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.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.
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 mailto:cooperr1@student.unimelb.edu.au
Reply-To:
Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1rvvIcWKOsJPNkArIKbeGDW1L0SxbC6TqCkNUNSsbGU5wwN... .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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 "$@" The recon-all.log is also attached.
I’ve also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable.
Do you have any idea what might be the problem?
Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached.
With warm regards, Rebecca Cooper
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Hi Yujing,
I guess not. This is the output:
cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 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:
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_512x256/002/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
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 mailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.au mailto:cooperr1@student.unimelb.edu.au > Sent: Friday, April 22, 2022 1:34 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edu mailto:YHUANG43@mgh.harvard.edu >; 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto: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.edu mailto:YHUANG43@mgh.harvard.edu > Sent: Friday, 22 April 2022 4:19 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Cc: cooperr1@student.unimelb.edu.au mailto: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.au mailto:cooperr1@student.unimelb.edu.au
Reply-To:
Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ylRzJnrmaICxgHmxf_M8Nza2cWBtKu30xn61W1QHOVn9V2... .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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: 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:
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_512x256/002/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
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.aumailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au> Sent: Friday, April 22, 2022 1:34 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu>; 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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: 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au> Sent: Saturday, April 23, 2022 2:44 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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:
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_512x256/002/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
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.aumailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au> Sent: Friday, April 22, 2022 1:34 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu>; 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Dear Yujing,
Thank you kindly for your support. Please see attached.
Kind regards,
*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:
https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnce...
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:
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_512x256/002/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
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.
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.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.
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 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1pFKSxeqmvvKC4crIOfp33MBLl8urhu2zGcbiK-_BpoX_sC... https://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
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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 [Image removed by sender.] Downloads.ziphttps://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web[Image removed by sender.]
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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/dcm2niixhttps://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au> Sent: Saturday, April 23, 2022 2:44 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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:
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_512x256/002/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
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.aumailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au> Sent: Friday, April 22, 2022 1:34 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu>; 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Dear Yujing,
My apologies! Hopefully you can access this now.
Kind regards, Rebecca
On Tue, Apr 26, 2022 at 11:29 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
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
*[image: Image removed by sender.] Downloads.zip https://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web**[image: Image removed by sender.]*
*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://secure-web.cisco.com/17Ga0Xp3SP-CwTjSyxKsZeuTrgi6PpoirdFYSw1C92Ho9db... https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix
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:
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_512x256/002/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
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. 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.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?
- 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 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1m4dzZ3yFrtYlPoet-IqOJhREM0ru1_1gtRFTMwcJAao1pX... https://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1TnkmooGsTg50ySLN3IOy_ax51hdQ8ejIhyMvJePzuTiSKY... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1m4dzZ3yFrtYlPoet-IqOJhREM0ru1_1gtRFTMwcJAao1pX... < https://secure-web.cisco.com/1m4dzZ3yFrtYlPoet-IqOJhREM0ru1_1gtRFTMwcJAao1pX... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Hi Rebecca,
I was able to access and download the data. But they don’t look like dicom files. They don’t have the prefix ‘DICM’ in them. Dcm2niix that I mentioned before doesn’t recognize them either.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Rebecca Elizabeth Cooper Sent: Tuesday, April 26, 2022 5:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution Dear Yujing,
My apologies! Hopefully you can access this now.
Kind regards, Rebecca
On Tue, Apr 26, 2022 at 11:29 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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 [Image removed by sender.] Downloads.ziphttps://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web[Image removed by sender.]
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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/dcm2niixhttps://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au> Sent: Saturday, April 23, 2022 2:44 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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:
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_512x256/002/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
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.aumailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.aumailto:cooperr1@student.unimelb.edu.au> Sent: Friday, April 22, 2022 1:34 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu>; 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto: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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/17JMXMuMvGAE1sBIMxYIQWrIfl8q3bZ6guhA5R7SvPKFiYn9baWdDJupVCIFhVpTT8HxhL8dycCbQjkttGhLXs8pQQH22jiRoRSMBDNP2i6P7nVfHfSBfRWn-FwxO3mcfqpaV_rZ7NmbSCx4S4DqTX1iwM9ImYJn8xmBWD7rx2Bow1NL0jo_DdSDSJDNsGB6BLvJjssSkpD1kIBkqOVO_BWaZYKUf37cXcAwlsi1afv_2pgCJf7ziCCtBBm3Q4FyDPqId2n0hGUJtIOoWTDN8rHIs2ZwyYSuQf3OqEYBJlriTR8b4z1syXH0D-9TLJP7I/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1TnkmooGsTg50ySLN3IOy_ax51hdQ8ejIhyMvJePzuTiSKYSQA0vP72Hd3frGNCc9ijqfJWIZIVGIEe6KHSZKH8KLfcyS5WMZEz9_11zWJ2MqWrSJeC9OCuROzXP2me-RCNGgnzUx-Tz592KvelZJu2qVzUBXW6R8npqIt8Yyv-GPPrmKPh7M4j7QUh2YWacVdAw859gDy-TtedCw5G9iG4ZhIYKcrDfiMhobvaM5uN036H-osRrKxn0kYedqt5Xfb-daB0p9huKWf95nhxZhaCd6gWiWc1ggyT7xCeHI5lgzTLEuUuiQPFGRvmhK91IvnN-e0hA8WH_pGAIqWghRPA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1m4dzZ3yFrtYlPoet-IqOJhREM0ru1_1gtRFTMwcJAao1pXp5jtofbxCZb6eRE4VOuHCZo1O541woEwbWc3xYognGEzH0KgVEAKU2TA3n1GflrqhBJtbL7mp4SehPUkLB2M131oAIqS3Li6umBLhN5DnSe_T-dfSMTkeelFiU9pggHVo6iq0Zrrz8e2T8vqr_8De4zYfZUinRKsu_7mFhim1raUVyBZ9CHDBJmsuh-3HB1lzUCrCSDKxEHG3VFPuyjEWMK2cMdvm19Z1oK7rYrzwjKgpOcI9w0Xsasib0xqYGIrpV8qS_PVEY8-A3QOG7uOXSpe8tX8fsdxK8eciKlw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1m4dzZ3yFrtYlPoet-IqOJhREM0ru1_1gtRFTMwcJAao1pXp5jtofbxCZb6eRE4VOuHCZo1O541woEwbWc3xYognGEzH0KgVEAKU2TA3n1GflrqhBJtbL7mp4SehPUkLB2M131oAIqS3Li6umBLhN5DnSe_T-dfSMTkeelFiU9pggHVo6iq0Zrrz8e2T8vqr_8De4zYfZUinRKsu_7mFhim1raUVyBZ9CHDBJmsuh-3HB1lzUCrCSDKxEHG3VFPuyjEWMK2cMdvm19Z1oK7rYrzwjKgpOcI9w0Xsasib0xqYGIrpV8qS_PVEY8-A3QOG7uOXSpe8tX8fsdxK8eciKlw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Dear Yujing,
I had the same problem with Dcm2niix, but I can open and extract them with dcm2nii. I’m not sure what that means!
Best,
Rebecca
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Thursday, 28 April 2022 2:26 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error
Hi Rebecca,
I was able to access and download the data. But they don’t look like dicom files. They don’t have the prefix ‘DICM’ in them. Dcm2niix that I mentioned before doesn’t recognize them either.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > On Behalf Of Rebecca Elizabeth Cooper Sent: Tuesday, April 26, 2022 5:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Dear Yujing,
My apologies! Hopefully you can access this now.
Kind regards,
Rebecca
On Tue, Apr 26, 2022 at 11:29 PM Huang, Yujing <YHUANG43@mgh.harvard.edu mailto:YHUANG43@mgh.harvard.edu > wrote:
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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all error
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Dear Yujing,
Thank you kindly for your support. Please see attached.
Kind regards,
Rebecca
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto: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:
https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/12H2e8xCjrEi-wbb98756SfSMuEwEOb12bspDfWR5MA902F...
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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of cooperr1@student.unimelb.edu.au mailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.au mailto:cooperr1@student.unimelb.edu.au > Sent: Saturday, April 23, 2022 2:44 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all error
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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:
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_512x256/002/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
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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto:cooperr1@student.unimelb.edu.au <cooperr1@student.unimelb.edu.au mailto:cooperr1@student.unimelb.edu.au > Sent: Friday, April 22, 2022 1:34 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edu mailto:YHUANG43@mgh.harvard.edu >; 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu mailto: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.edu mailto:YHUANG43@mgh.harvard.edu > Sent: Friday, 22 April 2022 4:19 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Cc: cooperr1@student.unimelb.edu.au mailto: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.au mailto:cooperr1@student.unimelb.edu.au
Reply-To:
Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu 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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freesurfer@nmr.mgh.harvard.edu
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cooperr1＠student.unimelb.edu.au -
Huang, Yujing -
Rebecca Elizabeth Cooper