Created SC1056 (markdown)

SC1056.md

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+#!/bin/bash
+set -e
+
+#Define your working directory
+export WDIR=/media/dongling/dongling/dpabi_FC/example_MNI
+
+TR=2
+remove_num=10
+remain_num=166
+Fwmh=4
+
+for n in pat #car
+do
+{
+
+for i in 17 #((i=1;i<=35;i++));
+do
+{
+num=$(echo $i|awk '{printf("%03d\n",$0)}')
+
+funcDIR=${WDIR}/FunRaw/${n}_${num} #directory of func dicom files
+strucDIR=${WDIR}/T1w/${n}_${num} #directory of T1w nii
+
+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
+
+#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