run.sh

#!/bin/bash

set -e
set -x

#cuda/nvidia drivers comes from the host. it needs to be mounted by singularity
export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64:$LD_LIBRARY_PATH

source /etc/fsl/5.0/fsl.sh #enable fsl (fsl6 still uses /etc/fsl/5.0.. for some reason)
export PATH=$PATH:/usr/lib/mrtrix/bin #enable mrtrix
export HOME=/ #so that tractseg uses /.tractseg not ~/.tractseg to look for prestaged models

opts=""
if [ $(jq -r .preprocess config.json) == "true" ]; then
	opts="$opts --preprocess"
fi

t1=`jq -r '.t1' config.json`
nr_fibers=`jq -r '.nr_fibers' config.json`

csd_type=`jq -r '.csd' config.json`
if [ $csd_type == "csd_msmt_5tt" ]; then
    if [ -f $t1 ]; then
	    echo "Error: csd_msmt_5tt requires a T1w image."
	    exit 1
    else
        ln -sf $t1 T1w_acpc_dc_restore_brain.nii.gz
    fi
    if [ $(jq -r .preprocess config.json) == "true" ]; then
	    echo "Error: csd_msmt_5tt doesn't work with --preprocess."
	    exit 1
    fi
fi

bundles=`jq -r '.bundles' config.json`
opts_bundles=""
if [ "$bundles" != "" ]; then
	opts_bundles="$opts_bundles --bundles $bundles"
fi

echo "(1/4) running tract_segmentation"
peaks=`jq -r '.peaks' config.json`
if [ -f $peaks ]; then

    echo "peaks.nii.gz found. Running TractSeg from peaks."
    cp $(jq -r .peaks config.json) tractseg_output/peaks.nii.gz

    TractSeg -i tractseg_output/peaks.nii.gz \
        --output_type tract_segmentation \
        --keep_intermediate_files \
        --nr_cpus 8 \
        -o tractseg_output 

else

    ln -sf $(jq -r .dwi config.json) dwi.nii.gz
    ln -sf $(jq -r .bvecs config.json) dwi.bvecs
    ln -sf $(jq -r .bvals config.json) dwi.bvals

    TractSeg -i dwi.nii.gz --raw_diffusion_input \
        --csd_type $(jq -r .csd config.json) \
        --output_type tract_segmentation \
        --keep_intermediate_files \
        --nr_cpus 8 \
        -o tractseg_output \
        $opts
           
fi

##Get segmentations of the regions were the bundles start and end (helpful for filtering fibers that do not run from start until end).
echo "(2/4) running endings_segmentation"
TractSeg -i tractseg_output/peaks.nii.gz \
    --output_type endings_segmentation \
    --nr_cpus 8 \
    -o tractseg_output \
    $opts

#For each bundle create a Tract Orientation Map (Wasserthal et al., Tract orientation mapping for bundle-specific tractography). 
#This gives you one peak per voxel telling you the main orientation of the respective bundle at this voxel. Can be used for 
#bundle-specific tracking (add option --track to generate streamlines). Needs around 22GB of RAM because for each bundle three 
#channels have to be stored (216 channels in total).

echo "(3/4) running TOM/tracking"
TractSeg -i tractseg_output/peaks.nii.gz \
    --output_type TOM \
    --nr_cpus 8 \
    -o tractseg_output \
    $opts

Tracking -i tractseg_output/peaks.nii.gz \
    --tracking_format tck \
    --nr_cpus 8 \
    --nr_fibers $nr_fibers \
    -o tractseg_output \
    $opts_bundles

##Tractometry is run over the peak_length.
echo "(4/4) running Tractometry"
Tractometry -i tractseg_output/TOM_trackings/ \
    -o tractseg_output/Tractometry_peaks.csv \
    -e tractseg_output/endings_segmentations/ \
    -s tractseg_output/peaks.nii.gz \
    --tracking_format tck \
    --TOM tractseg_output/TOM \
    --peak_length

echo "all done with tractseg"