neurodata/ndmg

#!/bin/bash

echo "Getting test data..."

loc="$PWD"
WARN=${PYTHONWARNINGS}
export PYTHONWARNINGS="ignore"

cd /tmp/
[ -f /tmp/ndmg_demo_dwi.zip ] || wget --quiet https://mrneurodata.s3.amazonaws.com/data/resources/ndmg_demo.zip
unzip -o /tmp/ndmg_demo.zip

ndmg_dwi_pipeline /tmp/ndmg_demo/sub-0025864/ses-1/dwi/sub-0025864_ses-1_dwi.nii.gz \
                  /tmp/ndmg_demo/sub-0025864/ses-1/dwi/sub-0025864_ses-1_dwi.bval \
                  /tmp/ndmg_demo/sub-0025864/ses-1/dwi/sub-0025864_ses-1_dwi.bvec \
                  /tmp/ndmg_demo/sub-0025864/ses-1/anat/sub-0025864_ses-1_T1w.nii.gz \
                  /tmp/ndmg_demo/MNI152NLin6_res-4x4x4_T1w.nii.gz \
                  /tmp/ndmg_demo/MNI152NLin6_res-4x4x4_T1w_brainmask.nii.gz \
                  /tmp/ndmg_demo/outputs \
                  /tmp/ndmg_demo/desikan-res-4x4x4.nii.gz


ndmg_bids /tmp/ndmg_demo/ /tmp/ndmg_demo/outputs/ group --hemispheres

echo "Path to qc fig: /tmp/ndmg_demo/outputs/qa/graphs/desikan-res-4x4x4/desikan-res-4x4x4_plot.html"

export PYTHONWARNINGS=${WARN}
cd "$loc"