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spinalcordtoolbox / sct_docker

Docker distribution of Spinal Cord Toolbox
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Batch_processing error with Docker_toolbox #28

Closed lrouhier closed 5 years ago

lrouhier commented 5 years ago

Description

batch_processing.sh return an error when running /home/sct/sct_4.0.0-beta.0/scripts/sct_process_segmentation.py -i t2_seg.nii.gz -p shape

Steps to Reproduce

  1. SCT V beta 4.0.0 on docker toolbox (docker pull)

  2. execute ./batch_processing.sh

Expected behavior: apply different fonction without problem

Actual behavior: stops when running sct_process_segmentation and yield the following error

IndexError: index 235 is out of bounds for axis 0 with size 235

full error here

jcohenadad commented 5 years ago

@lrouhier to rule out the possibility that the error has been fixed in recent versions of SCT, could you please create a container of SCT's master branch and try again with batch_processing under docker?

lrouhier commented 5 years ago

I will try that.

jcohenadad commented 5 years ago

@lrouhier any update?

lrouhier commented 5 years ago

There are no image for the container with the master branch I'm trying to create one.

jcohenadad commented 5 years ago

yes, that's precisely what i asked here ;-)

jcohenadad commented 5 years ago

@lrouhier any update?

lrouhier commented 5 years ago

With V4.0.0-beta5 (i wanted to try with the last stable release) There is no error. I think we can close the issue.