new stuff

layerfMRI · Apr 7, 2018 · 6f1e61f · 6f1e61f
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Showing 23 changed files with 4,274 additions and 1,008 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/DLPFC_Emily/.DS_Store b/DLPFC_Emily/.DS_Store
diff --git a/Up_sample_3d.sh b/Up_sample_3d.sh
@@ -16,7 +16,7 @@ echo "$sdelta_x"
 echo "$sdelta_y"
 echo "$sdelta_z"
 
-3dresample -dxyz $sdelta_x $sdelta_y $sdelta_z -rmode Li -overwrite -prefix scaled_$1 -input $1 
+3dresample -dxyz $sdelta_x $sdelta_y $sdelta_z -rmode Cu -overwrite -prefix scaled_$1 -input $1 
 
 echo "und tschuess"
 

diff --git a/anatomical_master_felix.sh b/anatomical_master_felix.sh
@@ -24,7 +24,7 @@ antsRegistration \
 --dimensionality 3  \
 --float 1  \
 --output [registered_,registered_Warped.nii.gz,registered_InverseWarped.nii.gz]   \
---interpolation Linear  \
+--interpolation BSpline[5]  \
 --use-histogram-matching 0   \
 --winsorize-image-intensities [0.005,0.995]   \
 --initial-moving-transform initial_matrix.txt    \

diff --git a/anatomical_master_mac.sh b/anatomical_master_mac.sh
@@ -23,7 +23,7 @@ antsRegistration \
 --float 0 \
 --collapse-output-transforms 1 \
 --output [registered_,registered_Warped.nii.gz,registered_InverseWarped.nii.gz] \
---interpolation Linear \
+--interpolation BSpline[5] \
 --use-histogram-matching 0 \
 --winsorize-image-intensities [0.005,0.995] \
 --initial-moving-transform initial_matrix.txt \

diff --git a/bias_field_corr/start_bias_field.sh b/bias_field_corr/start_bias_field.sh
@@ -11,6 +11,9 @@ cp /Users/huberl/NeuroDebian/repository/bias_field_corr/Bias_field_script_job.m
 
 3dcalc -a muncorr.nii -prefix muncorr.nii -overwrite -expr 'a' -datum short
 
+mv muncorr.nii bico_$1
+
+rm mucorr.nii
 rm uncorr.nii
 
 echo "und tschuess"
diff --git a/motion/.DS_Store b/motion/.DS_Store
diff --git a/motion/cross_da_moco/fix_start.sh b/motion/cross_da_moco/fix_start.sh
diff --git a/motion/cross_da_moco/moma.nii b/motion/cross_da_moco/moma.nii
diff --git a/motion/cross_da_moco/ninothree_mocobatch2run.m b/motion/cross_da_moco/ninothree_mocobatch2run.m
diff --git a/motion/cross_da_moco/ref_notnulled_AND.nii b/motion/cross_da_moco/ref_notnulled_AND.nii
diff --git a/motion/cross_da_moco/ref_notnulled_LEE.nii b/motion/cross_da_moco/ref_notnulled_LEE.nii
diff --git a/motion/cross_da_moco/ref_nulled_AND.nii b/motion/cross_da_moco/ref_nulled_AND.nii
diff --git a/motion/cross_da_moco/ref_nulled_LEE.nii b/motion/cross_da_moco/ref_nulled_LEE.nii
diff --git a/motion/cross_da_moco/start_MOCO_prep.sh b/motion/cross_da_moco/start_MOCO_prep.sh
diff --git a/motion/four_emily_mocobatch2run.m b/motion/four_emily_mocobatch2run.m
diff --git a/motion/four_tot_mocobatch2run.m b/motion/four_tot_mocobatch2run.m
diff --git a/motion/gnuplot_moco_multi.txt b/motion/gnuplot_moco_multi.txt
@@ -0,0 +1,36 @@
+#aufrufen mit load "./gnuplot.txt"
+
+
+#set terminal x11 enhanced 40
+set terminal postscript enhanced color solid  "Helvetica" 10
+
+set out "motion.ps"
+
+set key left bottom # f�r Position of Legend
+
+
+set title "Motion across timesteps"   font "Helvetica,10"
+set ylabel "displacement in mm"  font "Helvetica,10"
+set xlabel "|time in TR"  font "Helvetica,10"
+#set xrange [-2:2]
+#set yrange [-1:1]
+set size ratio 0.6
+#set grid
+#set ytics ("0" 0 , "1" 1, "-1" -1) 
+#set xtics (  "{/Symbol D} T" -85.37  , "-60.98" -60.98,  "-36.59" -36.59,  "-12.2" -12.2, "0" 0, "12.2" 12.2,  "36.59" 36.59,  "60.98" 60.98, "85.37" 85.37 )
+
+
+plot 	"rp_Basis_0a.txt" u 0:1  with lines  title "Not_nulled x"  linecolor rgb "green" ,\
+	"rp_Basis_0a.txt" u 0:2  with lines  title "Not_nulled y"  linecolor rgb "red" ,\
+	"rp_Basis_0a.txt" u 0:3  with lines  title "Not_nulled z"  linecolor rgb "brown" ,\
+	"rp_Basis_0b.txt" u 0:1  with lines  title "nulled x"  linecolor rgb "turquoise" ,\
+	"rp_Basis_0b.txt" u 0:2  with lines  title "nulled y"  linecolor rgb "pink" ,\
+	"rp_Basis_0b.txt" u 0:3  with lines  title "nulled z"  linecolor rgb "black" 
+
+#replot "plochsim_5_ohne.csv" using 1 with lines title "with eddy currents and  {/Symbol t} = 0.2 ms" linecolor rgb "blue"
+
+set term x11
+exit
+
+
+
diff --git a/motion/seven_eli_mocobatch2run.m b/motion/seven_eli_mocobatch2run.m
diff --git a/motion/start_moco_four_203.sh b/motion/start_moco_four_203.sh
@@ -0,0 +1,129 @@
+#!/bin/bash
+
+echo "fange an mit Bas"
+#!/bin/bash
+
+
+
+cp ./AMPL0.nii ./Basis_0a.nii
+cp ./AMPL0.nii ./Basis_0b.nii
+
+cp ./AMPL1.nii ./Basis_1a.nii
+cp ./AMPL1.nii ./Basis_1b.nii
+
+cp ./AMPL2.nii ./Basis_2a.nii
+cp ./AMPL2.nii ./Basis_2b.nii
+
+cp ./AMPL3.nii ./Basis_3a.nii
+cp ./AMPL3.nii ./Basis_3b.nii
+
+
+
+fslsplit ./Basis_0a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_0a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_0b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_0b.nii splited*
+
+rm splited*
+
+
+fslsplit ./Basis_1a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_1a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_1b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_1b.nii splited*
+
+rm splited*
+
+
+fslsplit ./Basis_2a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_2a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_2b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_2b.nii splited*
+
+rm splited*
+
+
+
+fslsplit ./Basis_3a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_3a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_3b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_3b.nii splited*
+
+rm splited*
+
+
+
+
+echo "hole SPM motion batch"
+cp /Users/huberl/NeuroDebian/repository/motion/four_tot_mocobatch2run.m ./four_tot_mocobatch2run.m
+/Applications/MATLAB_R2016a.app/bin/matlab -nodesktop -nosplash -r "four_tot_mocobatch2run"
+
+gnuplot "/Users/huberl/NeuroDebian/repository/motion/gnuplot_moco_multi.txt"
+
+#3dMean -prefix Not_Nulled_Basis_a.nii Not_Nulled_Basis_0a.nii Not_Nulled_Basis_1a.nii Not_Nulled_Basis_2a.nii Not_Nulled_Basis_3a.nii 
+#3dMean -prefix Nulled_Basis_b.nii Nulled_Basis_0b.nii Nulled_Basis_1b.nii Nulled_Basis_2b.nii Nulled_Basis_3b.nii 
+
+
+#afni_VASO_eval_SPM.sh
+
+echo "und tschuess"
diff --git a/motion/start_moco_four_331.sh b/motion/start_moco_four_331.sh
@@ -0,0 +1,129 @@
+#!/bin/bash
+
+echo "fange an mit Bas"
+#!/bin/bash
+
+
+
+cp ./AMPL0.nii ./Basis_0a.nii
+cp ./AMPL0.nii ./Basis_0b.nii
+
+cp ./AMPL1.nii ./Basis_1a.nii
+cp ./AMPL1.nii ./Basis_1b.nii
+
+cp ./AMPL2.nii ./Basis_2a.nii
+cp ./AMPL2.nii ./Basis_2b.nii
+
+cp ./AMPL3.nii ./Basis_3a.nii
+cp ./AMPL3.nii ./Basis_3b.nii
+
+
+
+fslsplit ./Basis_0a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_0a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_0b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_0b.nii splited*
+
+rm splited*
+
+
+fslsplit ./Basis_1a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_1a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_1b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_1b.nii splited*
+
+rm splited*
+
+
+fslsplit ./Basis_2a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_2a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_2b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_2b.nii splited*
+
+rm splited*
+
+
+
+fslsplit ./Basis_3a.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_3a.nii splited*
+
+rm splited*
+
+fslsplit ./Basis_3b.nii splited 
+
+cp splited0004.nii splited0000.nii
+cp splited0005.nii splited0001.nii
+cp splited0006.nii splited0002.nii
+cp splited0007.nii splited0003.nii
+
+fslmerge -t Basis_3b.nii splited*
+
+rm splited*
+
+
+
+
+echo "hole SPM motion batch"
+cp /Users/huberl/NeuroDebian/repository/motion/four_emily_mocobatch2run.m ./four_emily_mocobatch2run.m
+/Applications/MATLAB_R2016a.app/bin/matlab -nodesktop -nosplash -r "four_emily_mocobatch2run"
+
+gnuplot "/Users/huberl/NeuroDebian/repository/motion/gnuplot_moco_multi.txt"
+
+3dMean -prefix Not_Nulled_Basis_a.nii Not_Nulled_Basis_0a.nii Not_Nulled_Basis_1a.nii Not_Nulled_Basis_2a.nii Not_Nulled_Basis_3a.nii 
+3dMean -prefix Nulled_Basis_b.nii Nulled_Basis_0b.nii Nulled_Basis_1b.nii Nulled_Basis_2b.nii Nulled_Basis_3b.nii 
+
+
+afni_VASO_eval_SPM.sh
+
+echo "und tschuess"