updated scripts for Merima's second experiment

26afb813 · Alberto Lazari · 6d7638e7 · 26afb813 · 26afb813 · 26afb813
Commit 26afb813 authored Jan 07, 2022 by Alberto Lazari
--- a/Convert_2_MNC_T2w.sh
+++ b/Convert_2_MNC_T2w.sh
+#!/usr/bin/env bash
+
+# definitions
+workDir=/vols/Scratch/myelin/Mohamed/Merima_SecondExperiment_firstbatch
+scriptDir=/vols/Scratch/alazari/preclinicalMPM_scripts
+
+outDir=/vols/Scratch/myelin/Mohamed/Merima_SecondExperiment_firstbatch_preprocessed/
+mkdir -p $outDir
+mkdir -p $outDir/T2w
+exportDir=/vols/Scratch/myelin/Mohamed/Merima_SecondExperiment_firstbatch_preprocessed_export
+mkdir -p $exportDir
+mkdir -p $exportDir/T2w
+mkdir -p $exportDir/T2w/MNC
+
+
+subjList="MS07@20211008_154740_MS07_Merima_Doldcr_T2w_Diffusion_1_1
+MS08@20211011_201821_MS08_Merima_Doldcr_T2w_Diffusion_1_1
+MS09@20211012_174125_MS09_Merima_Doldcr_T2w_Diffusion_1_2
+MS10@20211013_180206_MS10_Merima_Doldcr_T2w_Diffusion_1_1
+MS11@20211014_162422_MS11_Merima_Doldcr_T2w_Diffusion_1_1
+MS12@20211015_180125_MS12_Merima_Doldcr_T2w_Diffusion_1_1
+MS13@20211018_175940_MS13_Merima_Doldcr_T2w_Diffusion_1_2
+MS14@20211019_174300_MS14_Merima_Doldcr_T2w_Diffusion_1_2
+MS15@20211021_200506_MS15_Merima_Doldcr_T2w_Diffusion_1_1
+MS16@20211022_151312_MS16_Merima_Doldcr_T2w_Diffusion_1_2
+MS17@20211026_172625_MS17_Merima_Doldcr_T2w_Diffusion_1_1
+MS18@20211027_203821_MS18_Merima_Doldcr_T2w_Diffusion_1_1
+MS19@20211029_154024_MS19b_Merima_Doldcr_T2w_Diffusion_1_1
+MS22@20211108_194315_MS22_Merima_Doldcr_T2w_Diffusion_4_1_5
+MS23@20211103_181935_MS23_Merima_Doldcr_T2w_Diffusion_1_1
+MS25@20211104_155453_MS25_Merima_Doldcd_T2w_Diffusion_1_1
+MS26@20211109_155744_MS26_Merima_Doldcr_T2w_Diffusion_1_1"
+
+# T2w is number 7
+# MS02@20210930_183625_MS02_MS02_Merima_Doldcr_T2w_Diffusion_1_1
+# MS03@20211004_193158_MS03_MS03_Merima_Doldcr_T2w_Diffusion_1_1
+# MS04@20211006_163600_MS04b_MS04_Merima_Doldcr_T2w_Diffusion_1_1
+# MS06@20211007_161034_MS06_MS06_Merima_Doldcr_T2w_Diffusion_1_1
+
+# T2w is number 5
+# MS07@20211008_154740_MS07_Merima_Doldcr_T2w_Diffusion_1_1
+# MS08@20211011_201821_MS08_Merima_Doldcr_T2w_Diffusion_1_1
+# MS09@20211012_174125_MS09_Merima_Doldcr_T2w_Diffusion_1_2
+# MS10@20211013_180206_MS10_Merima_Doldcr_T2w_Diffusion_1_1
+# MS11@20211014_162422_MS11_Merima_Doldcr_T2w_Diffusion_1_1
+# MS12@20211015_180125_MS12_Merima_Doldcr_T2w_Diffusion_1_1
+# MS13@20211018_175940_MS13_Merima_Doldcr_T2w_Diffusion_1_2
+# MS14@20211019_174300_MS14_Merima_Doldcr_T2w_Diffusion_1_2
+# MS15@20211021_200506_MS15_Merima_Doldcr_T2w_Diffusion_1_1
+# MS16@20211022_151312_MS16_Merima_Doldcr_T2w_Diffusion_1_2
+# MS17@20211026_172625_MS17_Merima_Doldcr_T2w_Diffusion_1_1
+# MS18@20211027_203821_MS18_Merima_Doldcr_T2w_Diffusion_1_1
+# MS19@20211029_154024_MS19b_Merima_Doldcr_T2w_Diffusion_1_1
+# MS22@20211108_194315_MS22_Merima_Doldcr_T2w_Diffusion_4_1_5
+# MS23@20211103_181935_MS23_Merima_Doldcr_T2w_Diffusion_1_1
+# MS25@20211104_155453_MS25_Merima_Doldcd_T2w_Diffusion_1_1
+# MS26@20211109_155744_MS26_Merima_Doldcr_T2w_Diffusion_1_1
+
+#"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 subjScan in $subjList; do
+
+  # separate the subject and the scan number
+  subj=${subjScan%@*}
+  scan=${subjScan#*@}
+
+  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
+
+  /vols/Data/postmort/dSSFP_process/bin/dSSFP_preprocess/unring $workDir/"$scan"/5/pdata/1/nifti/"$subj"*.nii $outDir/T2w/"$subj"_T2w_anat_unringed
+
+  #cp $workDir/"$subj"/T2w/"$subj"_T2w_anat_unringed.nii.gz $exportDir/T2w/"$subj"_T2w_anat_unringed.nii.gz
+
+  nii2mnc -quiet -signed -float $outDir/T2w/"$subj"_T2w_anat_unringed.nii $exportDir/T2w/MNC/"$subj"_T2w_anat.mnc
+
+echo "done"
+
+done
--- a/Convert_2_MNC.sh
+++ b/Convert_2_MNC.sh
--- a/GUIDE_step_by_step.md
+++ b/GUIDE_step_by_step.md
 # Mini-Guide

+# T2w 
+
+Just run the Convert_2_MNC_T2w.sh script
+
 # DIFFUSION

 Relevant scripts:

--- a/copy_niftis_and_mncs.sh
+++ b/copy_niftis_and_mncs.sh
@@ -3,21 +3,44 @@
 # definitions
 scriptDir=/vols/Scratch/alazari/preclinicalMPM_scripts/

-subjList="MS80@20210312_192904_MS80_Merima_Doldcr_T2w_Diffusion_1_3
-MS74@20210301_160217_MS74_MS74_MCAO_T2w_Diffusion_QSM_round2_1_3
-MS75@20210302_195833_MS75_MS74_MCAO_T2w_Diffusion_QSM_1_2
-MS95@20210315_184117_MS95_MS95_Merima_Doldcr_T2w_Diffusion_1_1
-MS76@20210303_164834_MS76_MS76_MCAO_T2w_Diffusion_QSM_round2_1_2
-MS78@20210304_165220_MS78_MS78_MCAO_T2w_Diffusion_QSM_round2_1_2
-MS77@20210316_193017_MS77_MS77_Merima_Doldcr_T2w_Diffusion_1_3
-MS93@20210305_205129_MS93_N_Merima_Doldcr_T2w_Diffusion_1_1
-MS86@20210308_191125_MS86_Merima_Doldcr_T2w_Diffusion_1_2
-MS94@20210317_190003_MS94_MS94_Merima_Doldcr_T2w_Diffusion_1_3
-MS88@20210309_174418_MS88_Merima_Doldcd_T2w_Diffusion_1_1
-MS79@20210311_174652_MS79_MS79_Merima_Doldcd_T2w_Diffusion_1_3
-MS73@20210322_155431_MS73_MS73_Merima_Doldcd_T2w_Diffusion_1_5
-MS87@20210323_182201_MS87_MS87_Merima_Doldcd_Tw2_Diffusion_1_6
-MS85@20210319_194410_MS85_MS85_Merima_Doldcr_T2w_Diffusion2_1_4"
+subjList="MS02@20210930_183625_MS02_MS02_Merima_Doldcr_T2w_Diffusion_1_1
+MS03@20211004_193158_MS03_MS03_Merima_Doldcr_T2w_Diffusion_1_1
+MS04@20211006_163600_MS04b_MS04_Merima_Doldcr_T2w_Diffusion_1_1
+MS06@20211007_161034_MS06_MS06_Merima_Doldcr_T2w_Diffusion_1_1
+MS07@20211008_154740_MS07_Merima_Doldcr_T2w_Diffusion_1_1
+MS08@20211011_201821_MS08_Merima_Doldcr_T2w_Diffusion_1_1
+MS09@20211012_174125_MS09_Merima_Doldcr_T2w_Diffusion_1_2
+MS10@20211013_180206_MS10_Merima_Doldcr_T2w_Diffusion_1_1
+MS11@20211014_162422_MS11_Merima_Doldcr_T2w_Diffusion_1_1
+MS12@20211015_180125_MS12_Merima_Doldcr_T2w_Diffusion_1_1
+MS13@20211018_175940_MS13_Merima_Doldcr_T2w_Diffusion_1_2
+MS14@20211019_174300_MS14_Merima_Doldcr_T2w_Diffusion_1_2
+MS15@20211021_200506_MS15_Merima_Doldcr_T2w_Diffusion_1_1
+MS16@20211022_151312_MS16_Merima_Doldcr_T2w_Diffusion_1_2
+MS17@20211026_172625_MS17_Merima_Doldcr_T2w_Diffusion_1_1
+MS18@20211027_203821_MS18_Merima_Doldcr_T2w_Diffusion_1_1
+MS19@20211029_154024_MS19b_Merima_Doldcr_T2w_Diffusion_1_1
+MS22@20211108_194315_MS22_Merima_Doldcr_T2w_Diffusion_4_1_5
+MS23@20211103_181935_MS23_Merima_Doldcr_T2w_Diffusion_1_1
+MS25@20211104_155453_MS25_Merima_Doldcd_T2w_Diffusion_1_1
+MS26@20211109_155744_MS26_Merima_Doldcr_T2w_Diffusion_1_1"
+
+
+# MS80@20210312_192904_MS80_Merima_Doldcr_T2w_Diffusion_1_3
+# MS74@20210301_160217_MS74_MS74_MCAO_T2w_Diffusion_QSM_round2_1_3
+# MS75@20210302_195833_MS75_MS74_MCAO_T2w_Diffusion_QSM_1_2
+# MS95@20210315_184117_MS95_MS95_Merima_Doldcr_T2w_Diffusion_1_1
+# MS76@20210303_164834_MS76_MS76_MCAO_T2w_Diffusion_QSM_round2_1_2
+# MS78@20210304_165220_MS78_MS78_MCAO_T2w_Diffusion_QSM_round2_1_2
+# MS77@20210316_193017_MS77_MS77_Merima_Doldcr_T2w_Diffusion_1_3
+# MS93@20210305_205129_MS93_N_Merima_Doldcr_T2w_Diffusion_1_1
+# MS86@20210308_191125_MS86_Merima_Doldcr_T2w_Diffusion_1_2
+# MS94@20210317_190003_MS94_MS94_Merima_Doldcr_T2w_Diffusion_1_3
+# MS88@20210309_174418_MS88_Merima_Doldcd_T2w_Diffusion_1_1
+# MS79@20210311_174652_MS79_MS79_Merima_Doldcd_T2w_Diffusion_1_3
+# MS73@20210322_155431_MS73_MS73_Merima_Doldcd_T2w_Diffusion_1_5
+# MS87@20210323_182201_MS87_MS87_Merima_Doldcd_Tw2_Diffusion_1_6
+# MS85@20210319_194410_MS85_MS85_Merima_Doldcr_T2w_Diffusion2_1_4

 for subjScan in $subjList; do

@@ -27,14 +50,14 @@ for subjScan in $subjList; do

  echo "copying and converting files for $subj"

-  workDir=/vols/Scratch/myelin/Mohamed/Merima_data_secondbatch_preprocessed/"$scan"
-  outDir=/vols/Scratch/myelin/Mohamed/Merima_data_secondbatch_preprocessed_export/NIFTI/"$subj"
-  outDirMNC=/vols/Scratch/myelin/Mohamed/Merima_data_secondbatch_preprocessed_export/MNC/"$subj"
+  workDir=/vols/Scratch/myelin/Mohamed/Merima_SecondExperiment_firstbatch_preprocessed/"$scan"
+  outDir=/vols/Scratch/myelin/Mohamed/Merima_SecondExperiment_firstbatch_preprocessed_export/NIFTI/"$subj"
+  outDirMNC=/vols/Scratch/myelin/Mohamed/Merima_SecondExperiment_firstbatch_preprocessed_export/MNC/"$subj"
  mkdir -p $outDir
  mkdir -p $outDirMNC

  # copy the average b0 (input for MBM for diffusion)
-  # cp $workDir/data_gibbs_eddy_b0_mean.nii.gz $outDir/"$subj"_data_gibbs_eddy_b0_mean.nii.gz
+  cp $workDir/data_gibbs_eddy_b0_mean.nii.gz $outDir/"$subj"_data_gibbs_eddy_b0_mean.nii.gz
  #
  # # copy the DTIFIT outputs
  # cp $workDir/dtifit_gibbs_eddy/dtifit_gibbs_eddy_MD.nii.gz $outDir/"$subj"_MD.nii.gz

--- a/core.27592
+++ b/core.27592
--- a/core.27594
+++ b/core.27594
--- a/core.3410
+++ b/core.3410
--- a/core.3412
+++ b/core.3412
--- a/core.41929
+++ b/core.41929
--- a/core.41932
+++ b/core.41932
--- a/diffpostproc_pipeline_full.sh
+++ b/diffpostproc_pipeline_full.sh
+#!/bin/bash
+module add mrdegibbs3d
+
+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 $jid1
+
+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 -d 1 -j $jid1 -nc -nd 64`
+jid2=`fsl_sub -q short.q -j $jid1 -l ${outputdir}/ deGibbs3D ${outputdir}/data.nii.gz ${outputdir}/data_gibbs.nii.gz `
+echo $jid2
+
+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 $jid3
+
+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 $jid4
+
+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 $jid5
+
+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 $jid6
+
+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 $jid7
+
+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}`
+echo $jid8
--- a/eddy_cuda8.0.e201589
+++ b/eddy_cuda8.0.e201589
--- a/eddy_cuda8.0.o201573
+++ b/eddy_cuda8.0.o201573
-
-Terminating program
--- a/eddy_cuda8.0.o201581
+++ b/eddy_cuda8.0.o201581
-EddyInputError:  Error when attempting to read --index file /vols/Scratch/myelin/Mohamed/Merima_data_secondbatch_preprocessed/20210301_160217_MS74_MS74_MCAO_T2w_Diffusion_QSM_round2_1_3/index.txt
-Terminating program
--- a/eddy_cuda8.0.o201589
+++ b/eddy_cuda8.0.o201589
-
-Terminating program
--- a/scan_identify.sh
+++ b/scan_identify.sh
 #!/usr/bin/env bash

 # definitions
-workDir=/vols/Scratch/myelin/Mohamed/Merima_data_firstbatch
-scriptDir=/vols/Scratch/alazari/preclinicalMPM_scripts/
-
-subjList="MS81_10_20200904"
+workDir=/vols/Scratch/myelin/Mohamed/Merima_SecondExperiment_firstbatch
+scriptDir=/vols/Scratch/alazari/preclinicalMPM_scripts/merima_pipelines/second_experiment_first_acquisition
+
+subjList="20210930_183625_MS02_MS02_Merima_Doldcr_T2w_Diffusion_1_1
+20211004_193158_MS03_MS03_Merima_Doldcr_T2w_Diffusion_1_1
+20211006_163600_MS04b_MS04_Merima_Doldcr_T2w_Diffusion_1_1
+20211007_161034_MS06_MS06_Merima_Doldcr_T2w_Diffusion_1_1
+20211008_154740_MS07_Merima_Doldcr_T2w_Diffusion_1_1
+20211011_201821_MS08_Merima_Doldcr_T2w_Diffusion_1_1
+20211012_174125_MS09_Merima_Doldcr_T2w_Diffusion_1_2
+20211013_180206_MS10_Merima_Doldcr_T2w_Diffusion_1_1
+20211014_162422_MS11_Merima_Doldcr_T2w_Diffusion_1_1
+20211015_180125_MS12_Merima_Doldcr_T2w_Diffusion_1_1
+20211018_175940_MS13_Merima_Doldcr_T2w_Diffusion_1_2
+20211019_174300_MS14_Merima_Doldcr_T2w_Diffusion_1_2
+20211021_200506_MS15_Merima_Doldcr_T2w_Diffusion_1_1
+20211022_151312_MS16_Merima_Doldcr_T2w_Diffusion_1_2
+20211026_172625_MS17_Merima_Doldcr_T2w_Diffusion_1_1
+20211027_203821_MS18_Merima_Doldcr_T2w_Diffusion_1_1
+20211029_154024_MS19b_Merima_Doldcr_T2w_Diffusion_1_1
+20211101_165313_MS20b_Merima_Doldcr_T2w_Diffusion_1_1
+20211108_194315_MS22_Merima_Doldcr_T2w_Diffusion_4_1_5
+20211103_181935_MS23_Merima_Doldcr_T2w_Diffusion_1_1
+20211104_155453_MS25_Merima_Doldcd_T2w_Diffusion_1_1
+20211109_155744_MS26_Merima_Doldcr_T2w_Diffusion_1_1"

 for subj in $subjList; do

@@ -16,7 +37,7 @@ for subj in $subjList; do

  echo "$a"

-  name=$(sed -n '11p' $workDir/"$subj"_Merima_Doldcr_T2w_Diffusion/"$a"/acqp)
+  name=$(sed -n '11p' $workDir/"$subj"/"$a"/acqp)
  echo "$a" "$name" >> $scriptDir/acquisition_order_"$subj".txt

  done

--- a/second_experiment_first_acquisition/acquisition_order_20210930_183625_MS02_MS02_Merima_Doldcr_T2w_Diffusion_1_1.txt
+++ b/second_experiment_first_acquisition/acquisition_order_20210930_183625_MS02_MS02_Merima_Doldcr_T2w_Diffusion_1_1.txt
+1 <1_Localizer>
+2 <1_Localizer>
+3 <1_Localizer_multi_slice>
+4 <MGE>
+5 <T2map_MSME>
+6 <1_Localizer_multi_slice>
+7 <T2_TurboRARE_3D>
+8 <win_DtiEpi_12>
+9 <win_DtiEpi_12>
+10 <win_DtiEpi_12>
+11 <mt_MGE_Nav_15>
+12 <mt_MGE_Nav_15>
+13 <1_Localizer>
+14 <1_Localizer_multi_slice>
+15 <MGE>
+16 
+17 
+18 
+19 
+20 
+21 
+22 
+23 
+24 
+25 
+26 
+27 
+28 
+29 
+30 
--- a/second_experiment_first_acquisition/acquisition_order_20211004_193158_MS03_MS03_Merima_Doldcr_T2w_Diffusion_1_1.txt
+++ b/second_experiment_first_acquisition/acquisition_order_20211004_193158_MS03_MS03_Merima_Doldcr_T2w_Diffusion_1_1.txt
+1 <1_Localizer>
+2 <1_Localizer>
+3 <1_Localizer_multi_slice>
+4 
+5 
+6 <1_Localizer_multi_slice>
+7 <T2_TurboRARE_3D>
+8 <win_DtiEpi_12>
+9 <win_DtiEpi_12>
+10 <win_DtiEpi_12>
+11 <mt_MGE_Nav_15>
+12 <mt_MGE_Nav_15>
+13 <1_Localizer_multi_slice>
+14 <1_Localizer_multi_slice>
+15 
+16 
+17 
+18 
+19 
+20 
+21 
+22 
+23 
+24 
+25 
+26 
+27 
+28 
+29 
+30 
--- a/second_experiment_first_acquisition/acquisition_order_20211006_163600_MS04b_MS04_Merima_Doldcr_T2w_Diffusion_1_1.txt
+++ b/second_experiment_first_acquisition/acquisition_order_20211006_163600_MS04b_MS04_Merima_Doldcr_T2w_Diffusion_1_1.txt
+1 <1_Localizer>
+2 <1_Localizer>
+3 <1_Localizer_multi_slice>
+4 <MGE>
+5 
+6 <1_Localizer_multi_slice>
+7 <T2_TurboRARE_3D>
+8 <win_DtiEpi_12>
+9 <win_DtiEpi_12>
+10 <win_DtiEpi_12>
+11 <mt_MGE_Nav_15>
+12 <mt_MGE_Nav_15>
+13 <1_Localizer>
+14 <1_Localizer>
+15 <1_Localizer_multi_slice>
+16 
+17 
+18 
+19 
+20 
+21 
+22 
+23 
+24 
+25 
+26 
+27 
+28 
+29 
+30 
--- a/second_experiment_first_acquisition/acquisition_order_20211007_161034_MS06_MS06_Merima_Doldcr_T2w_Diffusion_1_1.txt
+++ b/second_experiment_first_acquisition/acquisition_order_20211007_161034_MS06_MS06_Merima_Doldcr_T2w_Diffusion_1_1.txt
+1 <1_Localizer>
+2 <1_Localizer>
+3 <1_Localizer_multi_slice>
+4 
+5 
+6 <1_Localizer_multi_slice>
+7 <T2_TurboRARE_3D>
+8 <win_DtiEpi_12>
+9 <win_DtiEpi_12>
+10 <win_DtiEpi_12>
+11 <mt_MGE_Nav_15>
+12 <mt_MGE_Nav_15>
+13 <1_Localizer_multi_slice>
+14 
+15 
+16 
+17 
+18 
+19 
+20 
+21 
+22 
+23 
+24 
+25 
+26 
+27 
+28 
+29 
+30