README to include link to extended BIDS-compatible version, add Dockerfile and cleanup scripts

Dockerfile

@@ -0,0 +1 @@
+

README.md

@@ -1,3 +1,6 @@
+A BIDS-compatible extended version of this tool is available at https://github.com/mrfil/lesion-mapper-bids. The new version can utilize outputs from Freesurfer and/or fMRIPrep and distinguishes between deep white matter lesions and periventricular lesions.
+
+
 lesion_mapper - A tool for mappping white matter hyperintensities. Publication at: Wetter, Hubbard, Motl, Sutton. Brain Behav. 2016 Jan 28;6(3):e00440. https://doi.org/10.1002/brb3.440 
 
 For research purposes only! Please see LICENSE.txt
@@ -7,6 +10,9 @@ Brad Sutton <bsutton@illinois.edu>
 Magnetic Resonance Functional Imaging Lab <mrfil.bioen.illinois.edu>
 University of Illinois at Urbana-Champaign <illinois.edu>
 
+Create the directory structure for each participant's data before running.
+  This can be achieved using file_structure.sh
+
 Use: lesion_mapper -in <FLAIR image> [options]
 
 Required parameters:

file_structure.sh

@@ -0,0 +1,14 @@
+#!/bin/sh
+
+#Usage: Creates required directory structure for each subject in a list
+#Author: Paul B Camacho <pcamach2@illinois.edu>
+
+#run from subjects directory
+for SUB in 001 002 003 004 005
+do
+        mkdir ./${SUB}/Analyze/unbiased
+        mkdir ./${SUB}/Analyze/bet_notunbiased
+        mkdir ./${SUB}/Analyze/lesions_no2fast
+        mkdir ./${SUB}/Analyze/bet_multispectral
+        mkdir ./${SUB}/Analyze/sienax_no2fast
+done

fill_nw

@@ -46,7 +46,7 @@ if [ "$failed" = 1 ]; then
 fi
 
 # begin computation
-cluster --in=${mask} --thresh=0.5 -o ${mask}_cluster --no_table
+${FSLDIR}/bin/cluster --in=${mask} --thresh=0.5 -o ${mask}_cluster --no_table
 index_max=$(fslstats ${mask}_cluster -R | cut -d' ' -f2 | cut -d'.' -f1)
 index_cur=1
 while [ $index_cur -le $index_max ]

outputRemoval.sh

@@ -0,0 +1,20 @@
+#!/bin/sh
+
+#Usage: cleans out all results of pipeline_example except for dcm2niix outputs
+#Author: Paul B Camacho <pcamach2@illinois.edu>
+
+WorkDir=/path/to/dataDirectory
+
+for SUB in 001 002 003 004 005
+do
+	cd ${WorkDir}/${SUB}/Analyze/unbiased
+	rm ./*
+	cd ${WorkDir}/${SUB}/Analyze/bet_notunbiased
+	rm ./*
+	cd ${WorkDir}/${SUB}/Analyze/lesions_no2fast
+	rm ./*
+	cd ${WorkDir}/${SUB}/Analyze/bet_multispectral
+	rm ./*
+	cd ${WorkDir}/${SUB}/Analyze/sienax_no2fast
+	rm ./*
+done

pipeline_example

@@ -12,16 +12,19 @@ args="Js* TheraStride* Exert* METS* " #args="METS_[0-9][0-9]_[0-9][0-9][0-9][0-9
 args+="-numthreads auto -memory 32 -maxthreads 24 -analysis Analyze -v"
 #args=$subs+$args
 
-nwpipe "dcm2nii -m N ../SPACE" \
+nwpipe "dcm2niix -m N -x y -z y ../SPACE" \
     $args -numthreads 1 \
-    -in ../SPACE -out ../SPACE/o*.nii.gz
+    -in ../SPACE -out ../SPACE/*_Crop_1.nii.gz
 nwpipe "unbias T2.nii.gz" \
     $args -outdir unbiased \
-    -in ../SPACE/o*.nii.gz T2.nii.gz \
+    -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/o*.nii.gz T1.nii.gz \
+    -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 \

slicer_nw

@@ -53,7 +53,7 @@ if [ -n "$overlaycmd" ]; then
     overlay $overlaycmd
 fi
 
-    overlay 0 0 T2_unbiased -a lesionmapT2 0.9 1.1  lesionmapT2 0.9 1.1 overlay
+    overlay 0 0 ../unbiased/T2_unbiased.nii.gz -a ../lesions_no2fast/lesionmapT2.nii.gz 0.9 1.1  lesionmapT2 0.9 1.1 overlay
 
     midx=$(fslstats $in -C | cut -d" " -f1 | cut -d"." -f1)
     for it in {1..18}; do