pipeline_example

#!/bin/bash

echo "running pipeline"

homedir=$(pwd)
#args="lm_study_list.txt "
args="Js* TheraStride* Exert* METS* " #args="METS_[0-9][0-9]_[0-9][0-9][0-9][0-9][0-9][0-9] "
#args="METS_30_012313 "
#args="METS_30_012313 METS_22_040913 METS_01_062912 METS_10_071012 "
#args="METS_01_062912 "
#args+="-test "
args+="-numthreads auto -memory 32 -maxthreads 24 -analysis Analyze -v"
#args=$subs+$args

nwpipe "dcm2niix -m N -x y -z y ../SPACE" \
    $args -numthreads 1 \
    -in ../SPACE -out ../SPACE/*_Crop_1.nii.gz
nwpipe "unbias T2.nii.gz" \
    $args -outdir unbiased \
    -in ../SPACE/*_Crop_1.nii.gz T2.nii.gz \
    -out T2_unbiased.nii.gz
nwpipe "dcm2niix -m N -x y -z y ../MPRAGE" \
    $args -numthreads 1 \
    -in ../MPRAGE -out ../MPRAGE/*_Crop_1.nii.gz
nwpipe "unbias T1.nii.gz" \
    $args -outdir unbiased \
    -in ../MPRAGE/*_Crop_1.nii.gz T1.nii.gz \
    -out T1_unbiased.nii.gz
nwpipe "bet_nw ../unbiased/T2 t2_brain -R -png -d -s -m -f 0.4 -g -0.2" \
    $args -outdir bet_notunbiased \
    -in unbiased/T2.nii.gz \
    -out t2_brain.nii.gz
nwpipe "${NWTOOLS}/lesion_mapper -in ../bet_notunbiased/t2_brain.nii.gz -v -png -no2fast" \
    $args -outdir lesions_no2fast \
    -in bet_notunbiased/t2_brain.nii.gz \
    -out lesionmapT2.nii.gz \
    -out lesionstats.csv \
    -out lesions45.png
#nwpipe "${NWTOOLS}/lesion_mapper -in ../bet_notunbiased/t2_brain.nii.gz -v -png -no2fast" \
#    $args -outdir lesions_no2fast \
#    -in bet_notunbiased/t2_brain.nii.gz \
#    -in lesions8/t2_smooth.nii.gz t2_smooth.nii.gz \
#    -in lesions8/t2_seg_1.nii.gz t2_seg_1.nii.gz \
#    -in lesions8/t2_seg_0.nii.gz t2_seg_0.nii.gz \
#    -in lesions8/t2_restore.nii.gz t2_restore.nii.gz \
#    -in lesions8/MNItoT2.mat MNItoT2.mat \
#    -in lesions8/MNItoT2warp.nii.gz MNItoT2warp.nii.gz \
#    -in lesions8/wmt2.nii.gz wmt2.nii.gz \
#    -out lesionmapT2.nii.gz \
#    -out lesionstats.csv \
#    -out lesions45.png
nwpipe "bet_nw ../unbiased/T1_unbiased.nii.gz I_brain -IN2 ../unbiased/T2_unbiased.nii.gz -png -d -s -m -f 0.4 -g -0.2" \
    $args -outdir bet_multispectral \
    -in unbiased/T1_unbiased.nii.gz \
    -in unbiased/T2_unbiased.nii.gz \
    -out bet9.png
nwpipe "sienax_nw ../unbiased/T1_unbiased.nii.gz -o . -in2 ../unbiased/T2_unbiased.nii.gz -d -betdir ../bet_multispectral -lmt2 ../lesions_no2fast/lesionmapT2.nii.gz -nossm -S \"-N\"" \
    $args -outdir sienax_no2fast \
    -in unbiased/T1_unbiased.nii.gz \
    -in unbiased/T2_unbiased.nii.gz \
    -in lesions_no2fast/lesionmapT2.nii.gz \
    -out report.html \
    -out volumes.txt