Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

2019-05-01 Thread Glasser, Matthew 
External Email - Use Caution

To follow up on this, it seems the issue is related to where the data are 
stored on the user’s server and perhaps the filesystem/mode of access being 
used.  There does not seem to be any issue with Ubuntu generally, as processing 
works fine on the user’s OS drive…

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Jayasekera, Dinal" 
mailto:dinal.jayasek...@wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, April 11, 2019 at 12:11 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0


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Douglas,


I've run the recon-all script with images from patients that were previously 
run using FreeSurfer 5.3.0 and I received the same error.


I haven't run it outside of the HCP pipeline. I can attempt that to see if it 
gives a different result. I'm not exactly sure how to go about doing this. 
Could you advise me on the best sequence of actions to take?


Kind regards,
Dinal Jayasekera<https://dinaljay.weebly.com/>

PhD Candidate | InSITE Fellow<https://www.insitefellows.org/>
Ammar Hawasli Lab<https://hawaslilab.weebly.com/>
Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> 
| Washington University in St. Louis<https://wustl.edu/>


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>
Sent: Wednesday, April 10, 2019 5:27:15 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

Have you looked at the images to verify that there are no major problems
with it? Can you run it outside of the HCP pipeline to make sure it is
not an interaction?

On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:
>
> External Email - Use Caution
>
> Dear all,
>
>
> I have been running version 4 of the HCP Pipelines which now used
> FreeSurfer 6.0. I get the following error when running recon-all using
> their FreeSurferPipelineBatch script:
>
>
> /nu_evaluate: crashed while running minc_modify_header (termination
> status=134)/
> /nu_correct: crashed while running nu_evaluate (termination status=65280)/
> /ERROR: nu_correct/
>
> I didn't get this error previously when running FreeSurfer 5.3.0 on
> the same set of data. Are the MNI tools distributed through FreeSurfer
> 6.0 sensitive to the operating system and its version? Does anyone
> have a record of it working on an Ubuntu 14.04 OS?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
> 2) Platform: Ubuntu 14.04
> 3) recon-all.log: see attached
>
> Kind regards,
>
> *Dinal Jayasekera <https://dinaljay.weebly.com/>*
> *
> *
> PhD Candidate | InSITE Fellow <https://www.insitefellows.org/>
> Ammar Hawasli Lab <https://hawaslilab.weebly.com/>
> Department of Biomedical Engineering
> <https://bme.wustl.edu/Pages/default.aspx> | Washington University in
> St. Louis <https://wustl.edu/>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

2019-04-11 Thread Jayasekera, Dinal 
External Email - Use Caution

Douglas,


I've run the recon-all script with images from patients that were previously 
run using FreeSurfer 5.3.0 and I received the same error.


I haven't run it outside of the HCP pipeline. I can attempt that to see if it 
gives a different result. I'm not exactly sure how to go about doing this. 
Could you advise me on the best sequence of actions to take?


Kind regards,
Dinal Jayasekera<https://dinaljay.weebly.com/>

PhD Candidate | InSITE Fellow<https://www.insitefellows.org/>
Ammar Hawasli Lab<https://hawaslilab.weebly.com/>
Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> 
| Washington University in St. Louis<https://wustl.edu/>


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Wednesday, April 10, 2019 5:27:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

Have you looked at the images to verify that there are no major problems
with it? Can you run it outside of the HCP pipeline to make sure it is
not an interaction?

On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:
>
> External Email - Use Caution
>
> Dear all,
>
>
> I have been running version 4 of the HCP Pipelines which now used
> FreeSurfer 6.0. I get the following error when running recon-all using
> their FreeSurferPipelineBatch script:
>
>
> /nu_evaluate: crashed while running minc_modify_header (termination
> status=134)/
> /nu_correct: crashed while running nu_evaluate (termination status=65280)/
> /ERROR: nu_correct/
>
> I didn't get this error previously when running FreeSurfer 5.3.0 on
> the same set of data. Are the MNI tools distributed through FreeSurfer
> 6.0 sensitive to the operating system and its version? Does anyone
> have a record of it working on an Ubuntu 14.04 OS?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
> 2) Platform: Ubuntu 14.04
> 3) recon-all.log: see attached
>
> Kind regards,
>
> *Dinal Jayasekera <https://dinaljay.weebly.com/>*
> *
> *
> PhD Candidate | InSITE Fellow <https://www.insitefellows.org/>
> Ammar Hawasli Lab <https://hawaslilab.weebly.com/>
> Department of Biomedical Engineering
> <https://bme.wustl.edu/Pages/default.aspx> | Washington University in
> St. Louis <https://wustl.edu/>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] nu_correct crashing in FreeSurfer v6.0

2019-04-10 Thread Greve, Douglas N.,Ph.D. 
Have you looked at the images to verify that there are no major problems 
with it? Can you run it outside of the HCP pipeline to make sure it is 
not an interaction?

On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:
>
> External Email - Use Caution
>
> Dear all,
>
>
> I have been running version 4 of the HCP Pipelines which now used 
> FreeSurfer 6.0. I get the following error when running recon-all using 
> their FreeSurferPipelineBatch script:
>
>
> /nu_evaluate: crashed while running minc_modify_header (termination 
> status=134)/
> /nu_correct: crashed while running nu_evaluate (termination status=65280)/
> /ERROR: nu_correct/
>
> I didn't get this error previously when running FreeSurfer 5.3.0 on 
> the same set of data. Are the MNI tools distributed through FreeSurfer 
> 6.0 sensitive to the operating system and its version? Does anyone 
> have a record of it working on an Ubuntu 14.04 OS?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
> 2) Platform: Ubuntu 14.04
> 3) recon-all.log: see attached
>
> Kind regards,
>
> *Dinal Jayasekera *
> *
> *
> PhD Candidate | InSITE Fellow 
> Ammar Hawasli Lab 
> Department of Biomedical Engineering 
>  | Washington University in 
> St. Louis 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] nu_correct crashing in FreeSurfer v6.0

2019-04-08 Thread Jayasekera, Dinal 
External Email - Use Caution

Dear all,


I have been running version 4 of the HCP Pipelines which now used FreeSurfer 
6.0. I get the following error when running recon-all using their 
FreeSurferPipelineBatch script:


nu_evaluate: crashed while running minc_modify_header (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)
ERROR: nu_correct


I didn't get this error previously when running FreeSurfer 5.3.0 on the same 
set of data. Are the MNI tools distributed through FreeSurfer 6.0 sensitive to 
the operating system and its version? Does anyone have a record of it working 
on an Ubuntu 14.04 OS?


1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0

2) Platform: Ubuntu 14.04

3) recon-all.log: see attached

Kind regards,

Dinal Jayasekera

PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering 
| Washington University in St. Louis
Fri Apr  5 18:06:14 CDT 2019
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/NSI_27
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/FreeSurfer/custom/recon-all.v6.hires
-subjid NSI_27 -sd /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w -all -i /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -T2 /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T2w_acpc_dc_restore.nii.gz -emregmask /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2pial -openmp 8 -conf2hires
subjid NSI_27
setenv SUBJECTS_DIR /media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_27/T1w
FREESURFER_HOME /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6
Actual FREESURFER_HOME /home/functionalspinelab/Desktop/Dinal/Applications/freesurfer_6
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux fsl 4.4.0-142-generic #168~14.04.1-Ubuntu SMP Sat Jan 19 11:26:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  514029 
maxlocks unlimited
maxsignal514029 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem: 131691112  1286435243047588  52028   37652832   85154680
-/+ buffers/cache:5836012  125855100
Swap:  19989526641998288


program versions used
$Id: recon-all,v 1.580.2.15 2016/12/08 22:02:41 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/04/05-23:06:14-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: functionalspinelab  Machine: fsl  Platform: Linux  PlatformVersion: 4.4.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/04/05-23:06:14-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: functionalspinelab  Machine: fsl  Platform: Linux  PlatformVersion: 4.4.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/04/05-23:06:14-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: functionalspinelab  Machine: fsl  Platform: Linux  PlatformVersion: 4.4.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/04/05-23:06:14-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: functionalspinelab  Machine: fsl  Platform: Linux  PlatformVersion: 4.4.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2019/04/05-23:06:14-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: functionalspinelab  Machine: fsl  Platform: Linux