Nifti error in fastr script

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Mattias Hansson

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Apr 14, 2017, 6:37:05 AM4/14/17
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I get an error doing range matching: fastr says that a nii.gz file is not a valid nifti compressed file.


When I try to recreate the error with fastr execute, then there is no problem.


I am running the latest version of fastr develop.



[INFO] provenance:0139 >> DATA URI for: val://tmp/fastr_PROOF_XNAT_VolumeCalc_L_T0_o7_n08/n4_atlas/scan_9003406_20060322/__fastr_result__.pickle.gz?outputname=image&nr=0, job: <Job

  id=PROOF_XNAT_VolumeCalc_L_T0___n4_atlas___scan_9003406_20060322

  tool=n4.N4 1.6

  tmpdir=vfs://tmp/fastr_PROOF_XNAT_VolumeCalc_L_T0_o7_n08/n4_atlas/scan_9003406_20060322/>

[INFO] provenance:0139 >> DATA URI for: val://tmp/fastr_PROOF_XNAT_VolumeCalc_L_T0_o7_n08/range_mask_atlas/norm_mask_atlas_9003406_20060322/__fastr_result__.pickle.gz?outputname=output&nr=0&sampleid=norm_mask_atlas_9003406_20060322, job: <SourceJob

  id=PROOF_XNAT_VolumeCalc_L_T0___range_mask_atlas___norm_mask_atlas_9003406_20060322

  tmpdir=vfs://tmp/fastr_PROOF_XNAT_VolumeCalc_L_T0_o7_n08/range_mask_atlas/norm_mask_atlas_9003406_20060322/>

[INFO]       job:0732 >> Resetting current directory to /home/mhansson/fastr-scripts/PROOF_scripts

[WARNING]       job:0972 >> Output value [NiftiImageFileCompressed] "vfs://tmp/fastr_PROOF_XNAT_VolumeCalc_L_T0_o7_n08/rama_atlas/scan_9003406_20060322/image_0.nii.gz" not valid for datatype "NiftiImageFileCompressed"

[INFO]       job:0975 >> Data for output image is invalid

[WARNING]       job:0922 >> The output "image" is invalid!

MultiAtlasApp_PROOF_XNAT_volumeCalc_toQIB_Instance_LEFT_T0_out.txt

Martijn Starmans

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Apr 14, 2017, 6:44:40 AM4/14/17
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Are you sure your job finished and the output is written to the expected location? FASTR will also give you this error if a job is not finished, it does not necessary mean a datatype conflict. Happened to me when my FASTR job was cancelled by the cluster too to it using too much memory, which looking at our cluster queues is also the case for your job :). Running FASTR execute will then work because on the app node you DO have enough memory.

It would however be nice if FASTR had a separate error for when the data output is not found at all instead of reporting that the type is not valid.

Op vrijdag 14 april 2017 12:37:05 UTC+2 schreef Mattias Hansson:

Mattias Hansson

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Apr 14, 2017, 6:46:49 AM4/14/17
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Yes, good point. It may indeed be a memory issue. Will investigate.

Thanks!

Mattias Hansson

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Apr 14, 2017, 7:15:21 AM4/14/17
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Have investigated (increased memory on the node to 15G, from 6G). No change however, so I do believe this is something less trivial.

Mattias Hansson

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Apr 14, 2017, 8:02:29 AM4/14/17
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When I switched to the fastr develop module on the cluster, from using the latest version of fastr develop in a virtual env, then
this error does not appear.

Mattias Hansson

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Apr 14, 2017, 8:12:20 AM4/14/17
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Ofc, when i run using the fastr develop module, I cannot load dicoms from XNAT which does work in the latest version of develop.

Conclusion, I cannot run my code, for different reasons, using either the develop module or the latest version of develop in a virtual environment.
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