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create_axial_slices_of_C_maps
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create_axial_slices_of_C_maps
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#!/bin/bash
#bash ~/Documents/scripts/postmortembrain-mpm/Specific_analyses/EBC/MT_calibration/plot_C_slice_for_all
### writes out middle z slice of each sample for figure about variation
result_folder="/data/pt_02101/results/mt_calibration_7t"
#cd $result_folder
variation="MTvariation"
slicer_settings="-i 0 15 -z ${z_to_use}"
slicer_settings="-i $range -z 0.5"
for brain_slash_id in "009_C_W_HOIMA-2_mr_201112_Terra_7T_32Ch_WB" "018_C_C_TOJO_mr_200922_Terra_7T_32Ch_WB" "025_C_W_RAVEL_TAI_S_mr_200923_Terra_7T_32Ch_WB" "026_C_W_OSCAR_TAI_S_mr_200921_Terra_7T_32Ch_WB" "032_C_C_SAMSON_SL_TAC_mr_210206_Terra_7T_32Ch_WB"; do
z=.50
subfolder="${result_folder}/${brain_slash_id}"
c_file="${subfolder}/C_${variation}_variation_${brain_slash_id}_2p1_run01_brain_masked.nii"
c_perc_file="${subfolder}/C_in_perc_from_mean_${variation}_variation_${brain_slash_id}_2p1_run01_brain_masked.nii"
c_SE_perc_file="${subfolder}/C_SE_in_perc_${variation}_variation_${brain_slash_id}_2p1_run01_brain_masked.nii"
if [ -f ${orig_file} ]; then
#echo "slicing"
yes | rm killme*
range="0 1.4"
slicer_settings="-i $range -u -z $z"
slicer ${c_file} ${slicer_settings} ${result_folder}/${brain_slash_id}_mini_c.png
range="-15 15"
range="-10 10"
slicer_settings="-i $range -u -z $z"
slicer ${c_perc_file} ${slicer_settings} ${result_folder}/${brain_slash_id}_mini_cperc.png
range="0 7.5"
range="-10 10"
slicer_settings="-i $range -u -z $z"
slicer ${c_SE_perc_file} ${slicer_settings} ${result_folder}/${brain_slash_id}_mini_cse.png
pngappend ${result_folder}/${brain_slash_id}_mini_c.png + ${result_folder}/${brain_slash_id}_mini_cperc.png + ${result_folder}/${brain_slash_id}_mini_cse.png ${result_folder}/MTsat_${variation}_variation_${brain_slash_id}_C_slices_demonstration.png
fi
done
pngappend ${result_folder}/MTsat_MTvariation_variation_032_C_C_SAMSON_SL_TAC_mr_210206_Terra_7T_32Ch_WB_C_slices_demonstration.png - ${result_folder}/MTsat_MTvariation_variation_026_C_W_OSCAR_TAI_S_mr_200921_Terra_7T_32Ch_WB_C_slices_demonstration.png - ${result_folder}/MTsat_MTvariation_variation_025_C_W_RAVEL_TAI_S_mr_200923_Terra_7T_32Ch_WB_C_slices_demonstration.png - ${result_folder}/MTsat_MTvariation_variation_018_C_C_TOJO_mr_200922_Terra_7T_32Ch_WB_C_slices_demonstration.png - ${result_folder}/MTsat_MTvariation_variation_009_C_W_HOIMA-2_mr_201112_Terra_7T_32Ch_WB_C_slices_demonstration.png ${result_folder}/MTsat_MTvariation_variation_combined_slices_demonstration.png