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brainlife / app-removeTractOutliers

This is a brainlife.io wrapper app for mbaComputeFibersOutliers algorithm. It takes an existing tract classification and prune classified fibers that are unlike other fibers within the same tract.
MIT License
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Index exceeds matrix dimensions. #1

Open soichih opened 5 years ago

soichih commented 5 years ago

@DanNBullock I've merged the changes made to 1.2 branch to master, then added a code to copy surface directory from the input. The app (master branch) is failing with the following error message.

+ singularity exec -e docker://brainlife/mcr:neurodebian1604-r2017a ./compiled/wma_removeTractOutliers_BL
WARNING: docker-extract failed, missing executable or libarchive
WARNING: Will use old layer extraction method - this does not handle whiteouts
Index exceeds matrix dimensions.

Error in wma_classificationStrucGrouping>@(x)x(1:length(removalVec{iRemoveLabels})) (line 33)

Error in wma_classificationStrucGrouping (line 33)

Error in wma_formatForBrainLife_v2 (line 40)

Error in wma_removeTractOutliers_BL (line 45)

MATLAB:badsubscript

I am running with NKI A00010893 t1/dwi through TractSeg and running this App on the TractSeg output. Do you know what could be causing this error?

DanNBullock commented 5 years ago

Could you send me the input file, or a path to the directory with the inputs? I can just run it interactive and see what's actually going on.

On Thu, Jul 11, 2019 at 9:27 AM Soichi Hayashi notifications@github.com wrote:

@DanNBullock https://github.com/DanNBullock I've merged the changes made to 1.2 branch to master, then added a code to copy surface directory from the input. The app (master branch) is failing with the following error message.

  • singularity exec -e docker://brainlife/mcr:neurodebian1604-r2017a ./compiled/wma_removeTractOutliers_BL WARNING: docker-extract failed, missing executable or libarchive WARNING: Will use old layer extraction method - this does not handle whiteouts Index exceeds matrix dimensions.

Error in wma_classificationStrucGrouping>@(x)x(1:length(removalVec{iRemoveLabels})) (line 33)

Error in wma_classificationStrucGrouping (line 33)

Error in wma_formatForBrainLife_v2 (line 40)

Error in wma_removeTractOutliers_BL (line 45)

MATLAB:badsubscript

I am running with NKI A00010893 t1/dwi through TractSeg and running this App on the TractSeg output. Do you know what could be causing this error?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/brainlife/app-removeTractOutliers/issues/1?email_source=notifications&email_token=ADFXNPKQ7GVMOW5TCC3MGZTP64YK7A5CNFSM4IBF6MP2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G6UG22Q, or mute the thread https://github.com/notifications/unsubscribe-auth/ADFXNPLVHUSH54LBICOXSXDP64YK7ANCNFSM4IBF6MPQ .

soichih commented 5 years ago

Here it is

/N/dc2/projects/lifebid/hayashis/fordan/app-removeTractOutliers

You can test it locally by running the "main" script there.