Added initial scripts for LiFE

000_view_preprocessing_results

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+Check_preprocessing () {
+
+subj=$1
+
+low_res=/home/auguser2016/dMRI_DATA/PREPROCESSED_DATA/1.5mm_iso/$subj
+high_res=/home/auguser2016/dMRI_DATA/PREPROCESSED_DATA/0.75mm_iso/$subj
+
+# View denoising maps. The less anatomical structures are visible the better
+mrview $low_res/Temporal/Distortions/$subj\_series*
+
+# Compare DWI before and after denoising for each encoding direction
+mrview $low_res/Temporal/*AP.mif $low_res/Temporal/*AP_denoised.mif
+mrview $low_res/Temporal/*PA.mif $low_res/Temporal/*PA_denoised.mif
+
+# Compare mrtrix gradient for corrected DWI with original gradient table
+mrinfo $low_res/Temporal/$subj\_*AP_denoised.mif -export_grad_fsl $low_res/Temporal/bvecs $low_res/Temporal/bvals
+gedit $low_res/Temporal/bvecs &
+gedit $low_res/Temporal/Distortions/$subj\_gradients &
+gedit /home/auguser2016/dMRI_DATA/RAW_DATA/$subj*/s*/*ep2d*/*.bvec
+rm $low_res/Temporal/bvecs $low_res/Temporal/bvals
+
+# Compare DWI before and after dwipreproc
+mrview $low_res/Temporal/*AP.mif $low_res/Temporal/*PA.mif $low_res/Temporal/$subj\_denoised_preproc.mif
+
+# View mask used for bias field correction
+mrview $low_res/Temporal/$subj\_denoised_preproc.mif -overlay.load  $low_res/$subj\_clean_150mm_mask.mif -overlay.opacity 0.2 -overlay.colourmap 3
+
+# View bias field
+mrview $low_res/Temporal/Distortions/$subj\_bias_field.mif
+
+# View DWI before and after bias correction
+mrview $low_res/Temporal/$subj\_denoised_preproc.mif $low_res/$subj\_clean_150mm.mif
+
+# View normal and upsampled images
+mrview $low_res/$subj\_clean_150mm.mif $high_res/$subj\_clean_075mm.mif
+
+# View upsampled mask
+mrview $high_res/$subj\_clean_075mm.mif -overlay.load  $high_res/$subj\_clean_075mm_mask.mif -overlay.opacity 0.2 -overlay.colourmap 3
+
+# View SFR estimation voxels
+mrview $high_res/$subj\_clean_075mm.mif -overlay.load $high_res/Temporal/$subj\_clean_075mm_SFR_voxels.mif
+
+# View SFR
+shview $high_res/$subj\_clean_075mm_SFR.txt
+
+# View anatomical image overlaid on upsampled FOD
+mrview $high_res/$subj\_clean_075mm.mif $high_res/$subj\_075mm_anatomical_coreg2nodif_undist_2.nii.gz
+
+# View results of bet2
+mrview $high_res/$subj\_anatomical.nii.gz -overlay.load $high_res/Temporal/$subj\_anatomical_brain.nii.gz -overlay.opacity 0.3
+
+# View segmentation
+mrview $high_res/$subj\_075mm_anatomical_coreg2nodif_undist_2.nii.gz -overlay.load $high_res/$subj\_075mm_5tt.nii.gz -overlay.opacity 0.3
+
+# Correct WM segmentation in chiasm - modify opened ROI and close mrview. Modified WM segmentation image will be shown - repeat previous steps until satisfactory result is obtained. Terminate console to finish process
+mrview $high_res/$subj\_075mm_5tt.nii.gz -colourmap 3 -overlay.load $high_res/$subj\_075mm_anatomical_coreg2nodif_undist_2.nii.gz -overlay.colourmap 0 -overlay.opacity 0.8 -roi.load $high_res/$subj\_5tt_patch.mif
+
+5ttedit $high_res/$subj\_075mm_5tt.nii.gz -wm $high_res/$subj\_5tt_patch.mif $high_res/$subj\_5tt_for_act_modified.nii.gz -force
+
+while true; do
+  mrview $high_res/$subj\_5tt_for_act_modified.nii.gz -colourmap 3 -overlay.load $high_res/$subj\_075mm_anatomical_coreg2nodif_undist_2.nii.gz -overlay.colourmap 0 -overlay.opacity 0.8 -roi.load $high_res/$subj\_5tt_patch.mif
+  5ttedit $high_res/$subj\_075mm_5tt.nii.gz -wm $high_res/$subj\_5tt_patch.mif $high_res/$subj\_5tt_for_act_modified.nii.gz -force
+done
+
+}
+
+for i in /home/auguser2016/dMRI_DATA/PREPROCESSED_DATA/1.5mm_iso/*; do Check_preprocessing ${i: -4}; done

00_fsl_preprocess.sh

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+# Initializing
+
+# Folder with raw and preprocessed data
+data=/home/auguser2016/dMRI_DATA
+
+Preparation () {
+
+	# 2 resolutions (1.5 mm and 0.75mm), inside each folder all preprocessed data sets of corresponding resolution with masks, map of distortions etc.
+	a=${1::-6}
+
+	low_res=PREPROCESSED_DATA/1.5mm_iso/$a
+	high_res=PREPROCESSED_DATA/0.75mm_iso/$a
+
+	mkdir $data/$low_res
+	mkdir $data/$low_res/Temporal
+	mkdir $data/$low_res/Temporal/Distortions
+
+	mkdir $data/$high_res
+	mkdir $data/$high_res/Temporal
+
+
+	cd $data/RAW_DATA/${1::-1}/s*/
+
+	# Raw data files - DWI and anatomy - unpacked with MRIcron (dcm2nii) as a 4D Nifti images. Raw data goes: RAW_DATA/data_set_name/study.../studies_X/ where important are those with ep2d
+	# Transforming Nifti into .mif files and denoising them. Denoising is the very first that should be done - it's results can be viewed.
+
+	for b in *ep2d*; do
+		cd $b
+		mrconvert *a001.nii -stride -1,2,3,4 -fslgrad *.bvec *.bval $data/$low_res/Temporal/$a\_$b\.mif 
+		dwidenoise $data/$low_res/Temporal/$a\_$b.mif $data/$low_res/Temporal/$a\_$b\_denoised.mif -noise $data/$low_res/Temporal/Distortions/$a\_$b\_noise.mif -debug
+	  	cd ..
+	done
+
+	# Script from MRtrix interacting with fsl. Here version for correcting DWI with 2 phase encoding directions is used
+	dwipreproc AP  $data/$low_res/Temporal/*AP_denoised.mif -rpe_all $data/$low_res/Temporal/*PA_denoised.mif $data/$low_res/Temporal/$a\_denoised_preproc.mif -export_grad_mrtrix $data/$low_res/Temporal/Distortions/$a\_gradients 
+
+	# Masking preprocessed data. Results should be checked
+	dwi2mask $data/$low_res/Temporal/$a\_denoised_preproc.mif $data/$low_res/$a\_clean_150mm_mask.mif
+
+	# Masked is used for bias field correction using ANTS software
+	dwibiascorrect -ants $data/$low_res/Temporal/$a\_denoised_preproc.mif $data/$low_res/$a\_clean_150mm.mif -mask $data/$low_res/$a\_clean_150mm_mask.mif -bias $data/$low_res/Temporal/Distortions/$a\_bias_field.mif
+
+	# Preprocessing of 1.5 mm iso data sets done. Moving to upsampled resolution
+
+	# Upsampling by factor of 2 to 0.75mm. Justified step, in FBA even factor 3 can be recommended
+	mrresize $data/$low_res/$a\_clean_150mm.mif -scale 2.0 $data/$high_res/$a\_clean_075mm.mif
+
+	# Calculating mask again
+	dwi2mask $data/$high_res/$a\_clean_075mm.mif $data/$high_res/$a\_clean_075mm_mask.mif
+
+	# Estimating single fibre response (SFR) for default lmax
+	dwi2response tournier $data/$high_res/$a\_clean_075mm.mif $data/$high_res/$a\_clean_075mm_SFR.txt -shell 1600 -lmax 8 -mask $data/$high_res/$a\_clean_075mm_mask.mif -voxels $data/$high_res/Temporal/$a\_clean_075mm_SFR_voxels.mif
+
+	# Estimating FOD for previously obtained SFR
+	dwiextract $data/$high_res/$a\_clean_075mm.mif - | dwi2fod msmt_csd - $data/$high_res/$a\_clean_075mm_SFR.txt $data/$high_res/$a\_clean_075mm_FOD.mif -mask $data/$high_res/$a\_clean_075mm_mask.mif
+
+	# Performing coregistration of anatomical image to DWI images and segmenting it. It's easier approach as gradient table is not rotated this way. However for cross-modal studies it would be better to register DWI to anatomy
+
+	cd *MPRAGE*iso
+
+	# Converting DWI image from .mif to .nii.gz as FSL likes. This step should be checked as well.
+	mrconvert $data/$high_res/$a\_clean_075mm.mif $data/$high_res/Temporal/$a\_clean_075mm.nii.gz
+
+	# Coping anatomical image to corresponding folder
+	cp o* $data/$high_res/$a\_anatomical.nii.gz
+
+	# Extracting clean brain from anatomical image. Check this step
+	bet2 $data/$high_res/$a\_anatomical.nii.gz $data/$high_res/Temporal/$a\_anatomical_brain.nii.gz -f 0.6  	
+
+	# Corregister DWI to anatomy
+	epi_reg --epi=$data/$high_res/Temporal/$a\_clean_075mm.nii.gz --t1=$data/$high_res/$a\_anatomical.nii.gz --t1brain=$data/$high_res/Temporal/$a\_anatomical_brain.nii.gz --out=$data/$high_res/Temporal/$a\_nodif2mprage_2 --echospacing=0.00023 --pedir=-y
+
+	# Reverse corregistration matrix
+	convert_xfm -inverse $data/$high_res/Temporal/$a\_nodif2mprage_2.mat -omat $data/$high_res/Temporal/$a\_mprage2nodif_2.mat
+
+	# Apply reverted matrix to corregister anatomy to DWI
+	flirt -in $data/$high_res/$a\_anatomical.nii.gz -ref $data/$high_res/Temporal/$a\_clean_075mm.nii.gz -out $data/$high_res/$a\_075mm_anatomical_coreg2nodif_undist_2 -applyxfm -init $data/$high_res/Temporal/$a\_mprage2nodif_2.mat -interp sinc -sincwidth 7 -sincwindow hanning
+
+	# Perform segmentation into WM, GM, subcortical GM, CSF and possible pathological tissue using FIRST from FSL
+	5ttgen fsl $data/$high_res/$a\_075mm_anatomical_coreg2nodif_undist_2.nii.gz $data/$high_res/$a\_075mm_5tt.nii.gz
+
+}
+
+cd $data/RAW_DATA
+
+# List of all data_sets used in studies
+list=(fe21_1325/ hw91_0844/ ib57_0731/ kw99_0633/ lw37_0977/ nb30_1185/ ow93_0974/ ps94_1516/ rx88_1234/ sj22_1218/ ta14_1065/ tq63_1214/ xs62_1217/ xn78_1085/ uh47_1309/ uf97_1072/ ow93_0974/ )
+#list=(fe21_1325/)
+
+# This way 4 sets are processed at once - we can't process all at once due to RAM usage, however preprocessing one at a time is ineffective because e.g. eddy from dwipreproc is using only one core. There is a version of eddy operating on multicore processors, but it's not running on this machine
+
+for i in ${list[@]:0:3}; do Preparation $i & done
+wait
+for i in ${list[@]:3:6}; do Preparation $i & done
+wait
+for i in ${list[@]:6:9}; do Preparation $i & done
+wait
+for i in ${list[@]:9:12}; do Preparation $i & done
+wait
+for i in ${list[@]:12:15}; do Preparation $i & done
+wait
+for i in ${list[@]:15:18}; do Preparation $i & done
+wait
+for i in ${list[@]:18:21}; do Preparation $i & done
+wait
+for i in ${list[@]:21:24}; do Preparation $i & done
+wait
+for i in ${list[@]:24:27}; do Preparation $i & done
+wait
+for i in ${list[@]:27:30}; do Preparation $i & done
+wait
+for i in ${list[@]:30:33}; do Preparation $i & done
+wait
+
+# Returning to original folder
+cd /home/auguser2016/Scripts/
+

00_fsl_preprocess.sh~

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+# Initializing
+
+# Folder with raw and preprocessed data
+data=/home/auguser2016/dMRI_DATA
+
+Genral_preprocessing () {
+
+	# 2 resolutions (1.5 mm and 0.75mm), inside each folder all preprocessed data sets of corresponding resolution with masks, map of distortions etc.
+	a=${1::-6}
+
+	low_res=PREPROCESSED_DATA/1.5mm_iso/$a
+	high_res=PREPROCESSED_DATA/0.75mm_iso/$a
+
+	mkdir $data/$low_res
+	mkdir $data/$low_res/Temporal
+	mkdir $data/$low_res/Temporal/Distortions
+
+	mkdir $data/$high_res
+	mkdir $data/$high_res/Temporal
+
+
+	cd $data/RAW_DATA/${1::-1}/s*/
+
+	# Raw data files - DWI and anatomy - unpacked with MRIcron (dcm2nii) as a 4D Nifti images. Raw data goes: RAW_DATA/data_set_name/study.../studies_X/ where important are those with ep2d
+	# Transforming Nifti into .mif files and denoising them. Denoising is the very first that should be done - it's results can be viewed.
+
+	for b in *ep2d*; do
+		cd $b
+		mrconvert *a001.nii -stride -1,2,3,4 -fslgrad *.bvec *.bval $data/$low_res/Temporal/$a\_$b\.mif 
+		dwidenoise $data/$low_res/Temporal/$a\_$b.mif $data/$low_res/Temporal/$a\_$b\_denoised.mif -noise $data/$low_res/Temporal/Distortions/$a\_$b\_noise.mif -debug
+	  	cd ..
+	done
+
+	# Script from MRtrix interacting with fsl. Here version for correcting DWI with 2 phase encoding directions is used
+	dwipreproc AP  $data/$low_res/Temporal/*AP_denoised.mif -rpe_all $data/$low_res/Temporal/*PA_denoised.mif $data/$low_res/Temporal/$a\_denoised_preproc.mif -export_grad_mrtrix $data/$low_res/Temporal/Distortions/$a\_gradients 
+
+	# Masking preprocessed data. Results should be checked
+	dwi2mask $data/$low_res/Temporal/$a\_denoised_preproc.mif $data/$low_res/$a\_clean_150mm_mask.mif
+
+	# Masked is used for bias field correction using ANTS software
+	dwibiascorrect -ants $data/$low_res/Temporal/$a\_denoised_preproc.mif $data/$low_res/$a\_clean_150mm.mif -mask $data/$low_res/$a\_clean_150mm_mask.mif -bias $data/$low_res/Temporal/Distortions/$a\_bias_field.mif
+
+	# Preprocessing of 1.5 mm iso data sets done. Moving to upsampled resolution
+
+	# Upsampling by factor of 2 to 0.75mm. Justified step, in FBA even factor 3 can be recommended
+	mrresize $data/$low_res/$a\_clean_150mm.mif -scale 2.0 $data/$high_res/$a\_clean_075mm.mif
+
+	# Calculating mask again
+	dwi2mask $data/$high_res/$a\_clean_075mm.mif $data/$high_res/$a\_clean_075mm_mask.mif
+
+	# Estimating single fibre response (SFR) for default lmax
+	dwi2response tournier $data/$high_res/$a\_clean_075mm.mif $data/$high_res/$a\_clean_075mm_SFR.txt -shell 1600 -lmax 8 -mask $data/$high_res/$a\_clean_075mm_mask.mif -voxels $data/$high_res/Temporal/$a\_clean_075mm_SFR_voxels.mif
+
+	# Estimating FOD for previously obtained SFR
+	dwiextract $data/$high_res/$a\_clean_075mm.mif - | dwi2fod msmt_csd - $data/$high_res/$a\_clean_075mm_SFR.txt $data/$high_res/$a\_clean_075mm_FOD.mif -mask $data/$high_res/$a\_clean_075mm_mask.mif
+
+	# Performing coregistration of anatomical image to DWI images and segmenting it. It's easier approach as gradient table is not rotated this way. However for cross-modal studies it would be better to register DWI to anatomy
+
+	cd *MPRAGE*iso
+
+	# Converting DWI image from .mif to .nii.gz as FSL likes. This step should be checked as well.
+	mrconvert $data/$high_res/$a\_clean_075mm.mif $data/$high_res/Temporal/$a\_clean_075mm.nii.gz
+
+	# Coping anatomical image to corresponding folder
+	cp o* $data/$high_res/$a\_anatomical.nii.gz
+
+	# Extracting clean brain from anatomical image. Check this step
+	bet2 $data/$high_res/$a\_anatomical.nii.gz $data/$high_res/Temporal/$a\_anatomical_brain.nii.gz -f 0.6  	
+
+	# Corregister DWI to anatomy
+	epi_reg --epi=$data/$high_res/Temporal/$a\_clean_075mm.nii.gz --t1=$data/$high_res/$a\_anatomical.nii.gz --t1brain=$data/$high_res/Temporal/$a\_anatomical_brain.nii.gz --out=$data/$high_res/Temporal/$a\_nodif2mprage_2 --echospacing=0.00023 --pedir=-y
+
+	# Reverse corregistration matrix
+	convert_xfm -inverse $data/$high_res/Temporal/$a\_nodif2mprage_2.mat -omat $data/$high_res/Temporal/$a\_mprage2nodif_2.mat
+
+	# Apply reverted matrix to corregister anatomy to DWI
+	flirt -in $data/$high_res/$a\_anatomical.nii.gz -ref $data/$high_res/Temporal/$a\_clean_075mm.nii.gz -out $data/$high_res/$a\_075mm_anatomical_coreg2nodif_undist_2 -applyxfm -init $data/$high_res/Temporal/$a\_mprage2nodif_2.mat -interp sinc -sincwidth 7 -sincwindow hanning
+
+	# Perform segmentation into WM, GM, subcortical GM, CSF and possible pathological tissue using FIRST from FSL
+	5ttgen fsl $data/$high_res/$a\_075mm_anatomical_coreg2nodif_undist_2.nii.gz $data/$high_res/$a\_075mm_5tt.nii.gz
+
+}
+
+cd $data/RAW_DATA
+
+# List of all data_sets used in studies
+list=(fe21_1325/ hw91_0844/ ib57_0731/ kw99_0633/ lw37_0977/ nb30_1185/ ow93_0974/ ps94_1516/ rx88_1234/ sj22_1218/ ta14_1065/ tq63_1214/ xs62_1217/ xn78_1085/ uh47_1309/ uf97_1072/ ow93_0974/ )
+#list=(fe21_1325/)
+
+# This way 4 sets are processed at once - we can't process all at once due to RAM usage, however preprocessing one at a time is ineffective because e.g. eddy from dwipreproc is using only one core. There is a version of eddy operating on multicore processors, but it's not running on this machine
+
+for i in ${list[@]:0:3}; do Preparation $i & done
+wait
+for i in ${list[@]:3:6}; do Preparation $i & done
+wait
+for i in ${list[@]:6:9}; do Preparation $i & done
+wait
+for i in ${list[@]:9:12}; do Preparation $i & done
+wait
+for i in ${list[@]:12:15}; do Preparation $i & done
+wait
+for i in ${list[@]:15:18}; do Preparation $i & done
+wait
+for i in ${list[@]:18:21}; do Preparation $i & done
+wait
+for i in ${list[@]:21:24}; do Preparation $i & done
+wait
+for i in ${list[@]:24:27}; do Preparation $i & done
+wait
+for i in ${list[@]:27:30}; do Preparation $i & done
+wait
+for i in ${list[@]:30:33}; do Preparation $i & done
+wait
+
+# Returning to original folder
+cd /home/auguser2016/Scripts/
+