From 615a323066ac91d2077b1a3f97eca5a51549a112 Mon Sep 17 00:00:00 2001
From: Martin Bagge / brother <brother@bsnet.se>
Date: Thu, 27 Aug 2020 22:09:50 +0200
Subject: [PATCH] Updated SC1056 (markdown)

---
 SC1056.md | 114 +++++++-----------------------------------------------
 1 file changed, 14 insertions(+), 100 deletions(-)

diff --git a/SC1056.md b/SC1056.md
index fda1514..57529c0 100644
--- a/SC1056.md
+++ b/SC1056.md
@@ -1,108 +1,22 @@
-#!/bin/bash
-set -e
+## Expected a '}'. If you have one, try a ; or \\n in front of it.
 
-#Define your working directory
-export WDIR=/media/dongling/dongling/dpabi_FC/example_MNI
+NEEDS WORK. Adding the boiler plate to avoid confusion.
 
-TR=2
-remove_num=10
-remain_num=166
-Fwmh=4
+### Problematic code:
 
-for n in pat #car
-do
-{
+```sh
+true
+```
 
-for i in 17 #((i=1;i<=35;i++));
-do
-{
-num=$(echo $i|awk '{printf("%03d\n",$0)}')
+### Correct code:
 
-funcDIR=${WDIR}/FunRaw/${n}_${num} #directory of func dicom files
-strucDIR=${WDIR}/T1w/${n}_${num} #directory of T1w nii
+```sh
+true
+```
+### Rationale:
 
-mkdir ${WDIR}/ROI/${n}_${num}
-mkdir ${WDIR}/ROI/${n}_${num}/sub_roi
-mkdir ${WDIR}/ROI/${n}_${num}/mni_roi
-mkdir ${WDIR}/FunImg/${n}_${num}
+?
 
-niiDIR=${WDIR}/FunImg/${n}_${num} #save the func nii files
-roiDIR=${WDIR}/ROI/${n}_${num} #save ROIs
+### Exceptions:
 
-#dcm2nii
-dcm2nii -t y -d n -x y -o ${niiDIR} ${funcDIR}
-
-#Alcohol part
-cd ${niiDIR}
-rename e*.nii.gz Afunc.nii.gz *
-fslroi Afunc Afunc_t ${remove_num} ${remain_num}
-echo 'The first 10 timepoints has been removed.'
-
-#Slicetiming
-slicetimer -i Afunc_t -o Afunc_ta -r 2 --odd
-echo 'Slice Timing: Get consistent acquisition time.'
-
-#Realignment
-mcflirt -in Afunc_ta -refvol 0 -mats -plots -stats
-echo 'Motion corrections: all timeseries were realigned to vol0'
-
-#Coregister
-cd ${strucDIR}
-bet 2*.nii brain -f 0.3 -n -m -R -B
-echo 'Skull stripped'
-
-flirt -ref brain -in ${niiDIR}/Afunc_ta_mcf -omat func2T1w.mat
-echo 'Func data has been coregistered to T1w img.'
-
-#Normalize
-flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz -in brain -omat T1w2MNI.mat
-fnirt --in=brain --aff=T1w2MNI.mat --cout=T1w2MNI_warp --config=${WDIR}/T1_MNI152_2mm.cnf
-echo 'T1w2MNI warp field has been acquired.'
-
-cd ${niiDIR}
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i Afunc_ta_mcf.nii --warp=${strucDIR}/T1w2MNI_warp  --premat=${strucDIR}/func2T1w.mat --out=MNI_func
-echo 'Func data has been normalized to MNI space.'
-cd ${strucDIR}
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i brain.nii.gz --warp=T1w2MNI_warp   --out=MNI_brain
-
-#Smooth
-sigma = ${Fwmh}/sqrt(8*log(2))
-fslmaths MNI_func -kernel gauss sigma -fmean mMNI_func
-
-#Temporal filtering
-#bandpass frequency:0.01-0.1Hz
-#hp_sigma=50
-#lp_sigma=5
-#fslmaths mMNI_func -bptf 50 5 stf_MNI_func
-
-#Acquire ROIs in Subject's Space
-cd ${strucDIR}
-run_first -i brain.nii.gz -t T1w2MNI.mat -n 60 -o sub_L_Caud -m /share/app/imaging/fsl/data/first/models_336_bin/L_Caud_bin.bmv
-run_first -i brain.nii.gz -t T1w2MNI.mat -n 60 -o sub_R_Caud -m /share/app/imaging/fsl/data/first/models_336_bin/R_Caud_bin.bmv
-
-run_first -i brain.nii.gz -t T1w2MNI.mat -n 60 -o sub_L_Accu -m /share/app/imaging/fsl/data/first/models_336_bin/L_Accu_bin.bmv
-run_first -i brain.nii.gz -t T1w2MNI.mat -n 60 -o sub_R_Accu -m /share/app/imaging/fsl/data/first/models_336_bin/R_Accu_bin.bmv
-
-run_first -i brain.nii.gz -t T1w2MNI.mat -n 60 -o sub_L_Puta -m /share/app/imaging/fsl/data/first/models_336_bin/05mm/L_Puta_05mm.bmv
-run_first -i brain.nii.gz -t T1w2MNI.mat -n 60 -o sub_R_Puta -m /share/app/imaging/fsl/data/first/models_336_bin/05mm/R_Puta_05mm.bmv
-mv sub* ${roiDIR}/sub_roi
-
-echo "ROIs of" ${n}_${num} "in T1w space has been acquired"
-
-#Sub to MNI
-cd ${roiDIR}/sub_roi
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i sub_L_Caud.nii.gz --warp=${strucDIR}/T1w2MNI_warp   --out=MNI_L_Caud
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i sub_R_Caud.nii.gz --warp=${strucDIR}/T1w2MNI_warp   --out=MNI_R_Caud
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i sub_L_Accu.nii.gz --warp=${strucDIR}/T1w2MNI_warp   --out=MNI_L_Accu
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i sub_R_Accu.nii.gz --warp=${strucDIR}/T1w2MNI_warp   --out=MNI_R_Accu
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i sub_L_Puta.nii.gz --warp=${strucDIR}/T1w2MNI_warp   --out=MNI_L_Puta
-applywarp -r ${FSLDIR}/data/standard/MNI152_T1_2mm.nii.gz -i sub_R_Puta.nii.gz --warp=${strucDIR}/T1w2MNI_warp   --out=MNI_R_Puta
-
-mv MNI* ${roiDIR}/mni_roi
-echo "ROIs of" ${n}_${num} "in MNI space has been acquired"
-
-
-}
-done
-}
-done
+?
\ No newline at end of file