Re: [HCP-Users] Troubleshooting error with gradunwarp

2019-06-27 Thread Glasser, Matthew 
Thanks Mike.

Matt.

From: "Harms, Michael" 
Date: Thursday, June 27, 2019 at 3:02 PM
To: "Jayasekera, Dinal" 
Cc: "Glasser, Matthew" 
Subject: Re: [HCP-Users] Troubleshooting error with gradunwarp


Hi Dinal,
This issue should be resolved with the commit that I just pushed to the master.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From: "Harms, Michael" 
Date: Thursday, June 27, 2019 at 12:35 PM
To: "Jayasekera, Dinal" , 
"hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Troubleshooting error with gradunwarp


Hi,
That sounds like this issue, which we haven’t patched quite yet:
https://github.com/Washington-University/HCPpipelines/issues/119

Incidentally, you must be running off code in the current master branch, rather 
than the formally tagged “v4.0.0” release 
(https://github.com/Washington-University/HCPpipelines/releases) since this 
isn’t any issue in the tagged release.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From:  on behalf of "Jayasekera, Dinal" 

Date: Thursday, June 27, 2019 at 12:05 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] Troubleshooting error with gradunwarp

Dear all,

I'm trying to troubleshoot an error that I'm getting when running v4.0 
PreFreeSurferPipelineBatch. I initially thought the error arose as a result of 
grandunwarp but I don't think that is the case anymore. This is the error I am 
receiving:

'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
 and 
'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
 are the same file

I have attached the full output to stdout. Any insights?

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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Re: [HCP-Users] Troubleshooting error with gradunwarp

2019-06-27 Thread Harms, Michael 

Hi,
That sounds like this issue, which we haven’t patched quite yet:
https://github.com/Washington-University/HCPpipelines/issues/119

Incidentally, you must be running off code in the current master branch, rather 
than the formally tagged “v4.0.0” release 
(https://github.com/Washington-University/HCPpipelines/releases) since this 
isn’t any issue in the tagged release.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From:  on behalf of "Jayasekera, Dinal" 

Date: Thursday, June 27, 2019 at 12:05 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] Troubleshooting error with gradunwarp

Dear all,

I'm trying to troubleshoot an error that I'm getting when running v4.0 
PreFreeSurferPipelineBatch. I initially thought the error arose as a result of 
grandunwarp but I don't think that is the case anymore. This is the error I am 
receiving:

'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
 and 
'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
 are the same file

I have attached the full output to stdout. Any insights?

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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HCP-Users@humanconnectome.org
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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
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[HCP-Users] Troubleshooting error with gradunwarp

2019-06-27 Thread Jayasekera, Dinal 
Dear all,

I'm trying to troubleshoot an error that I'm getting when running v4.0 
PreFreeSurferPipelineBatch. I initially thought the error arose as a result of 
grandunwarp but I don't think that is the case anymore. This is the error I am 
receiving:

'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
 and 
'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
 are the same file

I have attached the full output to stdout. Any insights?


Kind regards,
Dinal Jayasekera

PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering 
| Washington University in St. Louis

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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StudyFolder: /media/functionalspinelab/RAID/Data/Dinal/mystudy
Subjlist: NSI_21
EnvironmentScript: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/Examples/Scripts/SetUpHCPPipeline.sh
Run locally: TRUE
This script must be SOURCED to correctly setup the environment prior to running 
any of the other HCP scripts contained here
NSI_21
Found 1 T1w Images for subject NSI_21
Found 1 T2w Images for subject NSI_21
About to run 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/PreFreeSurfer/PreFreeSurferPipeline.sh
PreFreeSurferPipeline.sh: HCPPIPEDIR: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
PreFreeSurferPipeline.sh: FSLDIR: /usr/local/fsl
PreFreeSurferPipeline.sh: HCPPIPEDIR_Global: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/scripts
PreFreeSurferPipeline.sh: HCPPIPEDIR_PreFS: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/PreFreeSurfer/scripts
Thu Jun 27 10:57:36 CDT 2019:PreFreeSurferPipeline.sh: Platform Information 
Follows: 
Linux fsl2 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux
Thu Jun 27 10:57:36 CDT 2019:PreFreeSurferPipeline.sh: Parsing Command Line 
Options
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Finished Parsing Command 
Line Options
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: StudyFolder: 
/media/functionalspinelab/RAID/Data/Dinal/mystudy
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Subject: NSI_21
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wInputImages: 
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/unprocessed/3T/T1w_MPR1/NSI_21_3T_T1w_MPR1.nii.gz@
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wInputImages: 
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/unprocessed/3T/T2w_SPC1/NSI_21_3T_T2w_SPC1.nii.gz@
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wTemplate: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_0.7mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wTemplateBrain: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_0.7mm_brain.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wTemplate2mm: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_2mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wTemplate: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T2_0.7mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wTemplateBrain: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T2_0.7mm_brain.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wTemplate2mm: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T2_2mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: TemplateMask: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Template2mmMask: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: BrainSize: 150
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: FNIRTConfig: 
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/T1_2_MNI152_2mm.cnf
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: MagnitudeInputName: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: PhaseInputName: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: GEB0InputName: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: TE: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: 
SpinEchoPhaseEncodeNegative: 
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/unprocessed/3T/T1w_MPR1/NSI_21_3T_SpinEchoFieldMap_AP.nii.gz
Thu Jun 27 10:57:38 CDT