[Freesurfer] recon-all error: mri_cc

[cooperr1]

External Email - Use Caution

Dear FreeSurfer developers,

 

I'm attempting to run recon-all with the longitudinal stream, but one
subject (out of >500) fails recon-all (I've re-started many times). The
cross-sectional and base (i.e. steps 1 and 2 of the longitudinal processing)
have completed successfully; it's this final step that has the error. It
appears that the error lies in mri_cc.

The final lines of the recon-all.log are below:

 

#--

#@# CC Seg Wed Jun 29 14:56:47 AEST 2022

 

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V
Y

 

will read input aseg from aseg.auto_noCCseg.mgz

writing aseg with cc labels to aseg.auto.mgz

will write lta as
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta

reading aseg from
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz

error: No such file or directory

error: mri_cc: volume
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz
already has CC in it.

Run with -force to reprocess (not recommended)

 

@#@FSTIME  2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M 21240
F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78

@#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78

Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP
Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

 

recon-all -s
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V
Y exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022

 

 

Freesurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
(I have also attempted with version 7.1.0 with identical results)

Platform: centos7_x86_64

Recon-all.log: attached.

 

With thanks,

 

Rebecca

 



recon-all.log
Description: Binary data
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Re: [Freesurfer] recon-all error

[cooperr1]

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-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Thursday, 28 April 2022 2:26 AM
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Rebecca 
Elizabeth Cooper
Sent: Tuesday, April 26, 2022 5:59 PM
To: Freesurfer support list 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 mailto:yhuan...@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-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Rebecca 
Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list mailto: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-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Huang, Yujing
Sent: Tuesday, 26 April 2022 8:34 AM
To: Freesurfer support list 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-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' 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:

 

 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/12H2e8xCjrEi-wbb98756SfSMuEwEOb12bspDfWR5MA902FANozPWRbUXsyyL6gN9KEwHx6CuWYNCXonjEXr5aFAfX4Z006TCkWCN7_kN-Bjv4ICPa40hXz9vS2F6d2E_ioG7bqYAPbNvCaZSeJk0JFgxvlcdKvEAx-0cOry-Kpdvt353hndbN7tEkUP5i4Uz7INcDb-OIfQoShj0XmsIhvxzso9Mn_NE2Prbo9kL5JqJoATNSdkUJRceDyGRyu6yzSASHxlWOpixCofpkrEvy03AEtdN4sow1neidzbMCklPa4BDrej7-nKzW3GK_8-dXibJfTbfRkdMm1ayRQ13NQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix

 

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

 

Please note that  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-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of 
coope...@student.unimelb.edu.au   
mailto:coope...@student.unimelb.edu.au> >
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] recon-all error

[cooperr1]

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-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Friday, 22 April 2022 11:11 PM
To: 'Freesurfer support list' 
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  --d filetype

 

(Replace  with full path to dicom file.)

 

Thanks.

 

Yujing

 

From: coope...@student.unimelb.edu.au   
mailto:coope...@student.unimelb.edu.au> > 
Sent: Friday, April 22, 2022 1:34 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu> 
>; 'Freesurfer support list' 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 mailto:yhuan...@mgh.harvard.edu> 
> 
Sent: Friday, 22 April 2022 4:19 AM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Cc: coope...@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: 

Re: [Freesurfer] recon-all error

[cooperr1]

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  
Sent: Friday, 22 April 2022 4:19 AM
To: Freesurfer support list 
Cc: coope...@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: 

coope...@student.unimelb.edu.au  


Reply-To: 

Freesurfer support list   



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 
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Compliance HelpLine at 
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] recon-all error

[cooperr1]

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

 



recon-all.log
Description: Binary data
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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/complianceline 
 .
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 
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