added initial scripts

Convert_2_MNC.sh

+#!/usr/bin/env bash
+
+# definitions
+workDir=/vols/Scratch/myelin/Mohamed/Merima_data_firstbatch_imported
+scriptDir=/vols/Scratch/alazari/preclinicalMPM_scripts
+
+mncDir=/vols/Scratch/myelin/Mohamed/Merima_data_firstbatch_imported/MNC
+mkdir -p $mncDir
+mkdir -p $mncDir/T2w
+mkdir -p $mncDir/DWI
+exportDir=/vols/Scratch/myelin/Mohamed/Merima_data_firstbatch_imported/Export
+mkdir -p $exportDir
+mkdir -p $exportDir/T2w
+mkdir -p $exportDir/DWI
+
+subjList="MS81_3_20200903"
+
+
+#"MS81_3_20200903"
+
+# "MS81_10_20200904
+# MS82_3_20200914
+# MS86_10_20200924
+# MS81_1_20200901
+# MS82_N_20200911
+# MS86_1_20200921
+# MS81_3_20200903
+# MS84_10_20200918
+# MS86_3_20200923
+# MS81_N_20200907
+# MS84_1_20200916
+# MS86_N_20200925
+# MS82_10_20200915
+# MS84_3_20200917
+# MS82_1_20200910
+# MS84_N_20200909"
+
+module add minc-toolkit-v1
+
+for subj in $subjList; do
+
+  echo "conversion to mnc format for $subj"
+
+  # /vols/Data/postmort/dSSFP_process/bin/dSSFP_preprocess/unring $workDir/"$subj"/T2w/MS81_3_Merima_Doldcr_T2w_Diffusion_Part2_7_1_1.nii $workDir/"$subj"/T2w/"$subj"_T2w_anat_unringed
+
+  /vols/Data/postmort/dSSFP_process/bin/dSSFP_preprocess/unring $workDir/"$subj"/T2w/"$subj"_T2w_anat.nii $workDir/"$subj"/T2w/"$subj"_T2w_anat_unringed
+
+  cp $workDir/"$subj"/T2w/"$subj"_T2w_anat_unringed.nii.gz $exportDir/T2w/"$subj"_T2w_anat_unringed.nii.gz
+
+  # cp $workDir/"$subj"/dtifit/"$subj"_FA.nii.gz $exportDir/DWI/"$subj"_FA.nii.gz
+  # cp $workDir/"$subj"/dtifit/"$subj"_MD.nii.gz $exportDir/DWI/"$subj"_MD.nii.gz
+  # cp $workDir/"$subj"/DWI_all/b0_mean.nii.gz $exportDir/DWI/"$subj"_b0_mean.nii.gz
+
+  # nii2mnc -quiet -signed -float $workDir/"$subj"/T2w/"$subj"_T2w_anat.nii $mncDir/T2w/"$subj"_T2w_anat.mnc
+  #
+  # nii2mnc -quiet -signed -float $workDir/"$subj"/dtifit/"$subj"_FA.nii.gz $mncDir/DWI/"$subj"_FA.mnc
+  # nii2mnc -quiet -signed -float $workDir/"$subj"/dtifit/"$subj"_MD.nii.gz $mncDir/DWI/"$subj"_MD.mnc
+  # nii2mnc -quiet -signed -float $workDir/"$subj"/DWI_all/b0_mean.nii.gz $mncDir/DWI/"$subj"_b0_mean.mnc
+
+echo "done"
+
+done

DWI_preprocess.sh

+#!/usr/bin/env bash
+
+# definitions
+workDir=/vols/Scratch/myelin/Mohamed/Merima_data_firstbatch_imported
+scriptDir=/vols/Scratch/alazari/preclinicalMPM_scripts/
+
+subjList="MS81_10_20200904"
+
+# "MS81_10_20200904
+# MS82_3_20200914
+# MS86_10_20200924
+# MS81_1_20200901
+# MS82_N_20200911
+# MS86_1_20200921
+# MS81_3_20200903
+# MS84_10_20200918
+# MS86_3_20200923
+# MS81_N_20200907
+# MS84_1_20200916
+# MS86_N_20200925
+# MS82_10_20200915
+# MS84_3_20200917
+# MS82_1_20200910
+# MS84_N_20200909"
+
+for subj in $subjList; do
+
+  echo "preprocessing diffusion for $subj"
+
+  # merge all scans
+
+  for i in {1..32}; do
+    printf "$workDir/"$subj"/DWI2/*_1_${i}.nii "  >> $workDir/"$subj"/DWI_filenames
+  done
+
+  for i in {1..32}; do
+    printf "$workDir/"$subj"/DWI3/*_1_${i}.nii "  >> $workDir/"$subj"/DWI_filenames
+  done
+
+  filelist=`cat $workDir/"$subj"/DWI_filenames`
+
+  fslmerge -t $workDir/data_merged $filelist
+
+
+
+  # cp $workDir/"$subj"_Merima_Doldcr_T2w_Diffusion/"$numberT2w"/pdata/1/nifti/*.nii  $outDir/"$subj"/T2w/"$subj"_T2w_anat.nii
+  #
+  # cp $workDir/"$subj"_Merima_Doldcr_T2w_Diffusion/"$numberQSM"/pdata/1/nifti/*.nii $outDir/"$subj"/QSM
+  #
+  #
+  # cp $workDir/"$subj"_Merima_Doldcr_T2w_Diffusion/"$numberDWI1"/pdata/1/nifti/*.nii $outDir/"$subj"/DWI1
+  #
+  # cp $workDir/"$subj"_Merima_Doldcr_T2w_Diffusion/"$numberDWI2"/pdata/1/nifti/*.nii $outDir/"$subj"/DWI2
+  #
+  #
+  # cp $workDir/"$subj"_Merima_Doldcr_T2w_Diffusion/"$numberDWI3"/pdata/1/nifti/*.nii $outDir/"$subj"/DWI3
+
+
+echo "done"
+
+done

DWI_preprocess_v2.sh

+#!/usr/bin/env bash
+
+# definitions
+workDir=/vols/Scratch/myelin/Mohamed/Merima_data_firstbatch_imported
+scriptDir=/vols/Scratch/alazari/preclinicalMPM_scripts
+
+subjList="MS81_10_20200904
+MS82_3_20200914
+MS86_10_20200924
+MS81_1_20200901
+MS82_N_20200911
+MS86_1_20200921
+MS81_3_20200903
+MS84_10_20200918
+MS86_3_20200923
+MS81_N_20200907
+MS84_1_20200916
+MS86_N_20200925
+MS82_10_20200915
+MS84_3_20200917
+MS82_1_20200910
+MS84_N_20200909"
+
+# "MS81_10_20200904
+# MS82_3_20200914
+# MS86_10_20200924
+# MS81_1_20200901
+# MS82_N_20200911
+# MS86_1_20200921
+# MS81_3_20200903
+# MS84_10_20200918
+# MS86_3_20200923
+# MS81_N_20200907
+# MS84_1_20200916
+# MS86_N_20200925
+# MS82_10_20200915
+# MS84_3_20200917
+# MS82_1_20200910
+# MS84_N_20200909"
+
+for subj in $subjList; do
+
+  echo "preprocessing diffusion for $subj"
+
+  # merge all scans
+  rm $workDir/"$subj"/DWI_filenames
+
+  for i in {1..32}; do
+    find "$workDir"/"$subj"/DWI2/*_1_${i}.nii >> $workDir/"$subj"/DWI_filenames
+  done
+
+  for i in {1..32}; do
+    find "$workDir"/"$subj"/DWI3/*_1_${i}.nii  >> $workDir/"$subj"/DWI_filenames
+  done
+
+  filelist=`cat $workDir/"$subj"/DWI_filenames`
+
+  mkdir -p $workDir/"$subj"/DWI_all
+  fslmerge -t $workDir/"$subj"/DWI_all/data_merged_original $filelist
+
+
+  # extract bvals and bvecs
+  $scriptDir/extract_bvecs_bvals.sh $workDir/"$subj"/bvals_bvecs
+
+  echo "orientation correction and mask generation for $subj"
+
+  cp $workDir/"$subj"/DWI_all/data_merged_original.nii.gz $workDir/"$subj"/DWI_all/data.nii.gz
+  fslorient -deleteorient $workDir/"$subj"/DWI_all/data.nii.gz
+  fslswapdim $workDir/"$subj"/DWI_all/data.nii.gz z -y x $workDir/"$subj"/DWI_all/data.nii.gz
+  fslorient -setsform 0.1 0 0 0 0 0.1 0 0 0 0 0.1 0 0 0 0 1 $workDir/"$subj"/DWI_all/data.nii.gz
+  fslorient -copysform2qform $workDir/"$subj"/DWI_all/data.nii.gz
+  fslorient -setsformcode 1 $workDir/"$subj"/DWI_all/data.nii.gz
+  fslorient -setqformcode 1 $workDir/"$subj"/DWI_all/data.nii.gz
+
+  mkdir $workDir/"$subj"/DWI_all/data_split
+  fslsplit $workDir/"$subj"/DWI_all/data.nii.gz $workDir/"$subj"/DWI_all/data_split/data -t
+  fslmerge -t $workDir/"$subj"/DWI_all/b0s_data $workDir/"$subj"/DWI_all/data_split/data0000.nii.gz $workDir/"$subj"/DWI_all/data_split/data0016.nii.gz $workDir/"$subj"/DWI_all/data_split/data0032.nii.gz $workDir/"$subj"/DWI_all/data_split/data0048.nii.gz
+
+  #mask generation
+  fslmaths $workDir/"$subj"/DWI_all/b0s_data -Tmean $workDir/"$subj"/DWI_all/b0_mean
+  fslmaths $workDir/"$subj"/DWI_all/b0_mean -thr 600 -dilM -ero -dilM -dilM -dilM -dilM -ero -ero -ero -bin $workDir/"$subj"/DWI_all/b0_mean_mask.nii.gz
+
+  echo "dtifits for $subj"
+  mkdir $workDir/"$subj"/dtifit
+  dtifit -k $workDir/"$subj"/DWI_all/data.nii.gz -m $workDir/"$subj"/DWI_all/b0_mean_mask.nii.gz -b $workDir/"$subj"/bvals_bvecs/bvals -r $workDir/"$subj"/bvals_bvecs/bvecs -o $workDir/"$subj"/dtifit/"$subj"
+
+echo "done"
+
+done

Fix_all_Dri.sh

+#!/usr/bin/env bash
+
+# definitions
+#workDir=/vols/Scratch/alazari/longitudinal_paTMS/resting_state
+workDir=/home/fs0/ndcn0979/scratch/Adrianna/BET
+scriptDir=/home/fs0/ndcn0979/scratch/Adrianna/Scripts
+fixDir=/home/fs0/ndcn0979/scratch/Adrianna/Scripts/fix
+module load fix
+
+#Do 03-3185 manually because of 176 thresholds
+for subj in 3185
+#1070 1079 3178 3179 3180 3181 3182 3183 3184 3186 3187 3189 3190 3191 3192 3193 3194 3195 3196 3197 3198 3199 3200 ;
+do
+  echo $subj
+
+    echo "FIX $subj"
+
+  for time in PRE POST FOLLOWUP;
+  do
+    echo $time
+
+# specify the subjects
+#subjList="
+#1070 1079 3178 3179 3180 3181 3182 3183 3184 3185 3186 3187 3189 3190 3191 3192 3193 3194 3195 3196 3197 3198 3199 3200"
+
+# Change permission
+echo change permission of folder
+  # chmod 777 $workDir/03-"$subj"/"$time"/RestingState/
+  # chmod 777 $workDir/03-"$subj"/"$time"/RestingState/*
+  # chmod 777 $workDir/03-"$subj"/"$time"/RestingState/*/*
+  # chmod 777 $workDir/03-"$subj"/"$time"/RestingState/*/*/*
+  # chmod 777 $workDir/03-"$subj"/"$time"/RestingState/*/*/*/*
+  # chmod 777 $workDir/03-"$subj"/"$time"/RestingState/*/*/*/*/*
+
+
+  # prepare the .sh file to apply FIX classifier for each fix_reg
+  $workDir/03-"$subj"/"$time"/RestingState/fix_reg.ica
+#Make sure you can find fix_reg.ica for each subj/time
+#find $workDir/03-"$subj"/"$time"/RestingState/fix_reg.ica # comment out the rest before you run
+
+  # Execute FIX
+  $fixDir/training_file/Standard.RData 5
+  fsl_sub -q veryshort.q fix $workDir/03-"$subj"/"$time"/RestingState/fix_reg.ica /home/fs0/home/ndcn0979/scratch/Adrianna/Scripts/fix/training_file/Standard.RData 5 -m -h -0
+
+
+
+  # Apply fix clean up
+  #   `fix_clean=` fsl_sub -q veryshort.q -j ${fix_classify} $fixDir/fix/fix -a $workDir/03-"$subj"/"$time"/RestingState/"$subj""$time"/"$subj"_"$time".ica/fix4melview_Rstandard_classifier_thr5.txt -m -h -0 done
+
+
+  #$workDir/03-"$subj"/"$time"/RestingState/"$subj""$time".fsf
+  #sed -i "s/XXX/"$subj"g" $workDir/03-"$subj"/"$time"/RestingState/"$subj""$time".fsf
+  #sed -i "s/YYY/"$time"g" $workDir/03-"$subj"/"$time"/RestingState/"$subj""$time".fsf
+
+  # run the .fsf design on feat
+  # fsl_sub -q short.q -s openmp,2 feat $workDir/"$subj"/"$subj"
+  #fsl_sub -q long.q -s openmp,2 feat $workDir/03-"$subj"/"$time"/RestingState/"$subj""$time"
+
+
+echo "done"
+
+done
+
+done

diffpostproc_pipeline_full.sh

+#!/bin/bash
+
+if [ $# -lt 4 ]
+then
+    echo "Usage: $0 inputdir exp_no_shell1 exp_no_shell2 exp_no_blipdown outputdir "
+    exit 0
+fi
+
+orient_corr () {
+fslorient -deleteorient $1
+fslswapdim $1 z -y x $1
+fslorient -setsform 0.1 0 0 0 0 0.1 0 0 0 0 0.1 0 0 0 0 1 $1
+fslorient -copysform2qform $1
+fslorient -setsformcode 1 $1
+fslorient -setqformcode 1 $1
+}
+
+inputdir=$1
+shell1=$2
+shell2=$3
+blipDown=$4
+outputdir=$5
+
+if [ -d "${outputdir}" ];
+then
+  echo "Output directory exists. Will work there."
+else
+  mkdir $5
+fi
+
+foldername=$(echo `basename ${inputdir}`)
+folderlength=`echo -n $foldername | wc -c`
+((folderlength = folderlength - 4))
+substring=$(echo `basename ${inputdir}` | cut -b 17-${folderlength})
+
+nofiles_shell1=`ls ${inputdir}/${shell1}/pdata/1/nifti/ -1 | wc -l`
+nofiles_shell2=`ls ${inputdir}/${shell2}/pdata/1/nifti/ -1 | wc -l`
+((nofiles = $nofiles_shell1 + $nofiles_shell2))
+
+echo merging all files
+for i in `seq 1 $nofiles_shell1`
+do
+  printf "$inputdir/${shell1}/pdata/1/nifti/${substring}_${shell1}_1_${i}.nii "  >> $outputdir/filenames
+done
+
+for i in `seq 1 $nofiles_shell2`
+do
+  printf "$inputdir/${shell2}/pdata/1/nifti/${substring}_${shell2}_1_${i}.nii "  >> $outputdir/filenames
+done
+
+filelist=`cat $outputdir/filenames`
+
+fslmerge -t ${outputdir}/data_merged_original $filelist
+
+cp /vols/Data/km/cetisca/scripts/diffpostproc_masterfiles/acp.txt ${outputdir}/acp.txt
+cp /vols/Data/km/cetisca/scripts/diffpostproc_masterfiles/index.txt ${outputdir}/index.txt
+cp /vols/Data/km/cetisca/scripts/diffpostproc_masterfiles/topup_mouse.cnf ${outputdir}/topup_mouse.cnf
+
+echo loading bvecs and bvals
+cp ${inputdir}/${shell1}/method ${outputdir}/method_shell1
+cp ${inputdir}/${shell2}/method ${outputdir}/method_shell2
+cp ${inputdir}/${blipDown}/pdata/1/nifti/${substring}_${blipDown}_1_1.nii ${outputdir}/b0_blipDown.nii
+/vols/Data/km/cetisca/functions/extract_bvecs_bvals.sh ${outputdir}
+
+echo queuing orientation correction and mask generation
+jid1=`fsl_sub -q veryshort.q -l ${outputdir}/logs1 /vols/Data/km/cetisca/scripts/diffpostproc_step1.sh ${outputdir}`
+
+echo queuing gibbs correction
+jid2=`/vols/Data/postmort/dSSFP_process/bin/dSSFP_preprocess/gibbs_correction_4D_clust ${outputdir}/data_gibbs.nii.gz -i ${outputdir}/data.nii.gz -l ${outputdir}/gibbslogs -j $jid1 -nc -nd 64`
+
+echo queuing pretopup file processing
+jid3=`fsl_sub -q veryshort.q -l ${outputdir}/logs3 -j $jid2 /vols/Data/km/cetisca/scripts/diffpostproc_step3.sh ${outputdir}`
+
+echo queuing topup
+jid4=`fsl_sub -q cuda.q -j $jid3 topup --imain=${outputdir}/b0_topup --datain=${outputdir}/acp.txt --config=${outputdir}/topup_mouse.cnf --out=${outputdir}/topup_mouse_output_2b0 --fout=${outputdir}/topup_mouse_field_2b0 --iout=${outputdir}/topup_mouse_unwarped_images_2b0 --logout=${outputdir}/topup_mouse_2b0.log --verbose`
+
+echo queuing post-topup file orientations
+jid5=`fsl_sub -q veryshort.q -l ${outputdir}/logs4 -j $jid4 /vols/Data/km/cetisca/scripts/diffpostproc_step4.sh ${outputdir}`
+
+echo queuing applytopup
+jid6=`fsl_sub -q veryshort.q -l ${outputdir}/logsapplytopup -j $jid5 applytopup --imain=${outputdir}/data_gibbs_cp --datain=${outputdir}/acp.txt --inindex=1 --topup=${outputdir}/topup_mouse_output_2b0 --method=jac --out=${outputdir}/data_gibbs_applytopup`
+
+echo queuing eddy cuda
+jid7=`fsl_sub -q cuda.q -j $jid5 eddy_cuda8.0 --imain=${outputdir}/data_gibbs_cp --mask=${outputdir}/b0_mean_mask_test.nii.gz --acqp=${outputdir}/acp.txt --index=${outputdir}/index.txt --bvecs=${outputdir}/bvecs_eddy --bvals=${outputdir}/bvals --topup=${outputdir}/topup_mouse_output_2b0 --out=${outputdir}/data_gibbs_eddy --verbose`
+
+echo queuing final file manipulations/organisations
+jid8=`fsl_sub -q short.q -l ${outputdir}/logs5 -j $jid7 /vols/Data/km/cetisca/scripts/diffpostproc_step5.sh ${outputdir}`

diffpostproc_step1.sh

+#!/bin/bash
+inputfolder=$1
+
+orient_corr () {
+fslorient -deleteorient $1
+fslswapdim $1 z -y x $1
+fslorient -setsform 0.1 0 0 0 0 0.1 0 0 0 0 0.1 0 0 0 0 1 $1
+fslorient -copysform2qform $1
+fslorient -setsformcode 1 $1
+fslorient -setqformcode 1 $1
+}
+
+cp ${inputfolder}/data_merged_original.nii.gz ${inputfolder}/data.nii.gz
+orient_corr ${inputfolder}/data.nii.gz
+
+mkdir ${inputfolder}/data_split
+fslsplit ${inputfolder}/data.nii.gz ${inputfolder}/data_split/data -t
+fslmerge -t ${inputfolder}/b0s_data ${inputfolder}/data_split/data0000.nii.gz ${inputfolder}/data_split/data0016.nii.gz ${inputfolder}/data_split/data0032.nii.gz ${inputfolder}/data_split/data0048.nii.gz
+
+#mask generation
+fslmaths ${inputfolder}/b0s_data -Tmean ${inputfolder}/b0_mean
+fslmaths ${inputfolder}/b0_mean -thr 600 -dilM -ero -dilM -dilM -dilM -dilM -ero -ero -ero -bin ${inputfolder}/b0_mean_mask.nii.gz

diffpostproc_step1_AL.sh

+#!/bin/bash
+inputfolder=$1
+
+orient_corr () {
+fslorient -deleteorient $1
+fslswapdim $1 z -y x $1
+fslorient -setsform 0.1 0 0 0 0 0.1 0 0 0 0 0.1 0 0 0 0 1 $1
+fslorient -copysform2qform $1
+fslorient -setsformcode 1 $1
+fslorient -setqformcode 1 $1
+}
+
+cp ${inputfolder}/data_merged_original.nii.gz ${inputfolder}/data.nii.gz
+orient_corr ${inputfolder}/data.nii.gz
+
+mkdir ${inputfolder}/data_split
+fslsplit ${inputfolder}/data.nii.gz ${inputfolder}/data_split/data -t
+fslmerge -t ${inputfolder}/b0s_data ${inputfolder}/data_split/data0000.nii.gz ${inputfolder}/data_split/data0016.nii.gz ${inputfolder}/data_split/data0032.nii.gz ${inputfolder}/data_split/data0048.nii.gz
+
+#mask generation
+fslmaths ${inputfolder}/b0s_data -Tmean ${inputfolder}/b0_mean
+fslmaths ${inputfolder}/b0_mean -thr 600 -dilM -ero -dilM -dilM -dilM -dilM -ero -ero -ero -bin ${inputfolder}/b0_mean_mask.nii.gz

diffpostproc_step5.sh

+#!/bin/bash
+
+inputfolder=$1
+
+fslswapdim ${inputfolder}/data_gibbs_applytopup x -z y ${inputfolder}/data_gibbs_applytopup
+fslswapdim ${inputfolder}/data_gibbs_eddy x -z y ${inputfolder}/data_gibbs_eddy
+
+#5th step: dtifit
+
+#dtifit
+mkdir ${inputfolder}/dtifit_gibbs_eddy
+dtifit -k ${inputfolder}/data_gibbs_eddy.nii.gz -m ${inputfolder}/b0_mean_mask.nii.gz -b ${inputfolder}/bvals -r ${inputfolder}/bvecs_zminxy -o ${inputfolder}/dtifit_gibbs_eddy/dtifit_gibbs_eddy
+
+mkdir ${inputfolder}/data_noddi_bpx
+cp ${inputfolder}/data_gibbs_eddy.nii.gz ${inputfolder}/data_noddi_bpx/data.nii.gz
+cp ${inputfolder}/b0_mean_mask.nii.gz ${inputfolder}/data_noddi_bpx/nodif_brain_mask.nii.gz
+cp ${inputfolder}/bvals ${inputfolder}/data_noddi_bpx/bvals
+cp ${inputfolder}/bvecs_zminxy ${inputfolder}/data_noddi_bpx/bvecs
+
+#check data is okay
+bedpostx_datacheck ${inputfolder}/data_noddi_bpx
+
+#6th step: bedpostx
+bedpostx ${inputfolder}/data_noddi_bpx
+
+#6th step: noddi
+
+#/home/fs0/amyh/func/run_NODDI.sh ${inputfolder}/data_noddi_bpx -m exvivo --dax 0.00056 --diso 0.001 --runMCMC

diffpostproc_step5_AL.sh

+#!/bin/bash
+
+inputfolder=$1
+
+#5th step: dtifit
+
+#dtifit
+mkdir ${inputfolder}/dtifit
+dtifit -k ${inputfolder}/data.nii.gz -m ${inputfolder}/b0_mean_mask.nii.gz -b ${inputfolder}/bvals -r ${inputfolder}/bvecs_zminxy -o ${inputfolder}/dtifit_gibbs_eddy/dtifit_gibbs_eddy
+
+
+# fslswapdim ${inputfolder}/data_gibbs_applytopup x -z y ${inputfolder}/data_gibbs_applytopup
+# fslswapdim ${inputfolder}/data_gibbs_eddy x -z y ${inputfolder}/data_gibbs_eddy
+#
+# #5th step: dtifit
+#
+# #dtifit
+# mkdir ${inputfolder}/dtifit_gibbs_eddy
+# dtifit -k ${inputfolder}/data_gibbs_eddy.nii.gz -m ${inputfolder}/b0_mean_mask.nii.gz -b ${inputfolder}/bvals -r ${inputfolder}/bvecs_zminxy -o ${inputfolder}/dtifit_gibbs_eddy/dtifit_gibbs_eddy
+
+# mkdir ${inputfolder}/data_noddi_bpx
+# cp ${inputfolder}/data_gibbs_eddy.nii.gz ${inputfolder}/data_noddi_bpx/data.nii.gz
+# cp ${inputfolder}/b0_mean_mask.nii.gz ${inputfolder}/data_noddi_bpx/nodif_brain_mask.nii.gz
+# cp ${inputfolder}/bvals ${inputfolder}/data_noddi_bpx/bvals
+# cp ${inputfolder}/bvecs_zminxy ${inputfolder}/data_noddi_bpx/bvecs
+
+# #check data is okay
+# bedpostx_datacheck ${inputfolder}/data_noddi_bpx
+#
+# #6th step: bedpostx
+# bedpostx ${inputfolder}/data_noddi_bpx
+
+#6th step: noddi
+
+#/home/fs0/amyh/func/run_NODDI.sh ${inputfolder}/data_noddi_bpx -m exvivo --dax 0.00056 --diso 0.001 --runMCMC

extract_bvecs_bvals.sh

+#### bvals
+foldername=$1
+
+grep -A8 PVM_DwEffBval= ${foldername}/method_shell1 | tail -n+2 | tr " " "\n" | sed '/^[[:space:]]*$/d' | sed -n '2{h; d}; 17{p; x;}; p' | tr -d " \t\r" > ${foldername}/bvals_b2.5k
+sed -n '/PVM_DwEffBval/,/PVM_DwGradVec/{ /PVM_DwEffBval/d; /PVM_DwGradVec/d; p }' ${foldername}/method_shell1 | tr " " "\n" | sed '/^[[:space:]]*$/d' | sed -n '2{h; d}; 17{p; x;}; p' | tr -d " \t\r"  > ${foldername}/bvals_b2.5k
+
+grep -A8 PVM_DwEffBval= ${foldername}/method_shell2 | tail -n+2 | tr " " "\n" | sed '/^[[:space:]]*$/d' | sed -n '2{h; d}; 17{p; x;}; p' | tr -d " \t\r"  > ${foldername}/bvals_b10k
+sed -n '/PVM_DwEffBval/,/PVM_DwGradVec/{ /PVM_DwEffBval/d; /PVM_DwGradVec/d; p }' ${foldername}/method_shell2 | tr " " "\n" | sed '/^[[:space:]]*$/d' | sed -n '2{h; d}; 17{p; x;}; p' | tr -d " \t\r"  > ${foldername}/bvals_b10k
+#
+###### extract text between two patterns with bash awk - patterns = "##$PVM_DwEffBval=( 32 )" and "##$PVM_DwGradVec=( 32, 3 )"
+#
+cat ${foldername}/bvals_b2.5k > ${foldername}/bvals2
+cat ${foldername}/bvals_b10k >> ${foldername}/bvals2
+cat ${foldername}/bvals2 | tr "\n" " " > ${foldername}/bvals
+
+sed -n '/##$PVM_DwDir=(/,/##$PVM_DwDgSwitch/{ /PVM_DwDir/d; /##$PVM_DwDgSwitch/d; p }' ${foldername}/method_shell1 | tr " " "\n" | sed '/^[[:space:]]*$/d' | tr -d " \t\r" | tr -d " \t\r" | tr "\n" " " | sed -e "s/\([^\ ]*\ [^\ ]*\ [^\ ]*\)\ /\1\\`echo -e '\n\r'`/g" | tr "\r" "\n" | sed '/^[[:space:]]*$/d' > ${foldername}/bvecs2.5k
+sed  -i '1 i\0 0 0' ${foldername}/bvecs2.5k
+sed  -i '16 a\0 0 0' ${foldername}/bvecs2.5k
+
+sed -n '/##$PVM_DwDir=(/,/##$PVM_DwDgSwitch/{ /PVM_DwDir/d; /##$PVM_DwDgSwitch/d; p }' ${foldername}/method_shell2 | tr " " "\n" | sed '/^[[:space:]]*$/d' | tr -d " \t\r" | tr -d " \t\r"| tr "\n" " " | sed -e "s/\([^\ ]*\ [^\ ]*\ [^\ ]*\)\ /\1\\`echo -e '\n\r'`/g" | tr "\r" "\n" | sed '/^[[:space:]]*$/d' > ${foldername}/bvecs10k
+sed  -i '1 i\0 0 0' ${foldername}/bvecs10k
+sed  -i '16 a\0 0 0' ${foldername}/bvecs10k
+
+cat ${foldername}/bvecs2.5k > ${foldername}/bvecs_temp
+cat ${foldername}/bvecs10k >> ${foldername}/bvecs_temp
+
+/vols/Data/km/aurea/TDP_M323K/Analysis/transpose_bvecs.sh ${foldername}/bvecs_temp >  ${foldername}/bvecs
+
+rm ${foldername}/bvals_b2.5k ${foldername}/bvals_b10k ${foldername}/bvals2 ${foldername}/bvecs_temp ${foldername}/bvecs2.5k ${foldername}/bvecs10k

first_acquisition/acquisition_order_MS81_10_20200904.txt

+1 <1_Localizer (E1)>
+2 <2_Localizer (E2)>
+3 <3_Localizer_multi_slice (E3)>
+4 <4_MGE_check_bubble (E4)>
+5 <5_T2map_MSME_25TE_nx5ms_highres (E5)>
+6 <6_Localizer_multi_slice_B0Map (E6)>
+7 <7_T2w_anat_res0.06 (E7)>
+8 <8_QSM_MGE_IES3ms_20TE (E8)>
+9 <9_win_DtiEpi_01_BlipDown (E9)>
+10 <10_win_DtiEpi_01_b2.5k (E10)>
+11 <11_win_DtiEpi_01_b10k (E11)>
+12 <1_Localizer (E12)>
+13 <1_Localizer (E13)>
+14 <1_Localizer (E14)>
+15 <1_Localizer (E15)>
+16 <1_Localizer (E16)>
+17 <1_Localizer (E17)>
+18 <6_Localizer_multi_slice_B0Map (E6)>
+19 
+20 
+21 
+22 
+23 
+24 
+25 
+26 
+27 
+28 
+29 
+30 

first_acquisition/acquisition_order_MS81_1_20200901.txt

+1 <1_Localizer (E1)>
+2 <2_Localizer (E2)>
+3 <3_Localizer_multi_slice (E3)>
+4 <4_MGE_check_bubble (E4)>
+5 <5_T2map_MSME_25TE_nx5ms_highres (E5)>
+6 <6_Localizer_multi_slice_B0Map (E6)>
+7 <7_T2w_anat_res0.06 (E7)>
+8 <8_QSM_MGE_IES3ms_20TE (E8)>
+9 <9_win_DtiEpi_01_BlipDown (E9)>
+10 <10_win_DtiEpi_01_b2.5k (E10)>
+11 <11_win_DtiEpi_01_b10k (E11)>
+12 <1_Localizer (E12)>
+13 <1_Localizer (E13)>
+14 <1_Localizer (E14)>
+15 <6_Localizer_multi_slice_B0Map (E6)>
+16 
+17 
+18 
+19 
+20 
+21 
+22 
+23 
+24 
+25 
+26 
+27 
+28 
+29 
+30 

first_acquisition/acquisition_order_MS81_3_20200903.txt

+1 <1_Localizer (E1)>
+2 
+3 
+4 
+5 
+6 
+7 <7_T2w_anat_res0.06 (E7)>
+8 <8_QSM_MGE_IES3ms_20TE (E8)>
+9 <9_win_DtiEpi_01_BlipDown (E9)>
+10 <10_win_DtiEpi_01_b2.5k (E10)>
+11 <11_win_DtiEpi_01_b10k (E11)>
+12 <3_Localizer_multi_slice_B0Map (E12)>
+13 <3_Localizer_multi_slice (E13)>
+14 <4_MGE_check_bubble (E14)>
+15 <5_T2map_MSME_25TE_nx5ms_highres (E15)>
+16 
+17 
+18 
+19 
+20 
+21 
+22 
+23 
+24 
+25 
+26 
+27 
+28 
+29 
+30 
+1 <1_Localizer (E1)>
+2 
+3 
+4 
+5 
+6 
+7 <7_T2w_anat_res0.06 (E7)>
+8 <8_QSM_MGE_IES3ms_20TE (E8)>
+9 <9_win_DtiEpi_01_BlipDown (E9)>
+10 <10_win_DtiEpi_01_b2.5k (E10)>
+11 <11_win_DtiEpi_01_b10k (E11)>
+12 <3_Localizer_multi_slice_B0Map (E12)>