running emsegmenter in a batch

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running emsegmenter in a batch

Tiffany Liu
Hi,

I would like to run the 'Emsegmenter with Atlas' module (MR human brain mode simple) in a script on a batch of cases. Should I use the python scripting environment or other alternative? If python, could you please point me a documentation describing parameters for the different variations of emsegment available in python (emsegment, emsegmentLogic, etc)? Thanks so much.

Best,

Tiffany
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Re: running emsegmenter in a batch

Kilian Pohl
Hi Tiffany,

There are a couple of resources - First

http://www.slicer.org/slicerWiki/index.php/Modules:EMSegment-Command-Line3.6

then if you execute in your Slicer-build directory

ctest -N -R EMS

it lists all the tests associated  with the EMSegmenter so if you then
run for example
ctest -VV -R EMSegCL_Task_BRAINS_MRIHumanBrain_scalartype_float_very_small

it shows you in the first line how to call EMSegmenter as a command line
, e.g.


/software/Slicer4/superbuild/Slicer-build/Slicer --launcher-no-splash
--launch
/software/Slicer4/superbuild/Slicer-build/lib/Slicer-4.2/cli-modules/EMSegmentCommandLine
--verbose --mrmlSceneFileName
/software/Slicer3/Slicer3/Modules/EMSegment/Tasks/MRI-Human-Brain.mrml
--targetVolumeFileNames
/software/Slicer4/superbuild/Slicer-build/MIDAS_Data/MRI-Human-Brain_T1-Atlas-Template-float_very_small.nrrd
--resultVolumeFileName
/software/Slicer4/superbuild/Slicer-build/Modules/Loadable/EMSegment/RESULT_BRAINS_MRI-Human-Brain_T1-Atlas-Template-float_very_small.nrrd
--taskPreProcessingSetting :C1:C0 --registrationPackage BRAINS
--registrationAffineType -1 --registrationDeformableType -1
--atlasVolumeFileNames
/software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/MRI-Human-Brain/very_small_atlas_skulneck.nrrd,/software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/MRI-Human-Brain/very_small_atlas_air.nrrd,/software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/MRI-Human-Brain/very_small_atlas_csf.nrrd,/software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/MRI-Human-Brain/very_small_atlas_greymatter.nrrd,/software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/MRI-Human-Brain/very_small_atlas_whitematter.nrrd,/software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/MRI-Human-Brain/very_small_atlas_t1.nrrd

Hope this helps

Kilian


On 05/01/2013 04:09 PM, Ting Liu wrote:

> Hi,
>
> I would like to run the 'Emsegmenter with Atlas' module (MR human brain mode simple) in a script on a batch of cases. Should I use the python scripting environment or other alternative? If python, could you please point me a documentation describing parameters for the different variations of emsegment available in python (emsegment, emsegmentLogic, etc)? Thanks so much.
>
> Best,
>
> Tiffany
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject

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