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s5_visualization_Orbital.sh
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s5_visualization_Orbital.sh
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#!/bin/bash
vglrun mrview \
-load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/nans.nii.gz \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/brain_glass.nii.gz \
-overlay.opacity 0.03 \
-overlay.colourmap 0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/Left-MDl_AND_Left-MDm.nii.gz \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_47s_dil-1.nii.gz \
-overlay.colour 31.0,119.0,180.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL22_clean.tck \
-tractography.lighting 1 \
-tractography.colour 31.0,119.0,180.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_47m_dil-1.nii.gz \
-overlay.colour 255.0,127.0,14.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL21_clean.tck \
-tractography.lighting 1 \
-tractography.colour 255.0,127.0,14.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_anterior_47r_dil-1.nii.gz \
-overlay.colour 44.0,160.0,44.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL20_clean.tck \
-tractography.lighting 1 \
-tractography.colour 44.0,160.0,44.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_11l_dil-1.nii.gz \
-overlay.colour 214.0,39.0,40.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL19_clean.tck \
-tractography.lighting 1 \
-tractography.colour 214.0,39.0,40.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_13l_dil-1.nii.gz \
-overlay.colour 148.0,103.0,189.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL23_clean.tck \
-tractography.lighting 1 \
-tractography.colour 148.0,103.0,189.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_anterior_10p_dil-1.nii.gz \
-overlay.colour 57.0,59.0,121.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL17_clean.tck \
-tractography.lighting 1 \
-tractography.colour 57.0,59.0,121.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_posterior_10p_dil-1.nii.gz \
-overlay.colour 107.0,110.0,207.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL16_clean.tck \
-tractography.lighting 1 \
-tractography.colour 107.0,110.0,207.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Polar_10p_dil-1.nii.gz \
-overlay.colour 99.0,121.0,57.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL18_clean.tck \
-tractography.lighting 1 \
-tractography.colour 99.0,121.0,57.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Area_10d_dil-1.nii.gz \
-overlay.colour 181.0,207.0,107.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL15_clean.tck \
-tractography.lighting 1 \
-tractography.colour 181.0,207.0,107.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_Orbital_Frontal_Complex_dil-1.nii.gz \
-overlay.colour 140.0,109.0,49.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL24_clean.tck \
-tractography.lighting 1 \
-tractography.colour 140.0,109.0,49.0 \
-overlay.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/flywheel/v0/output/RTP/fs/ROIs/L_posterior_OFC_Complex_dil-1.nii.gz \
-overlay.colour 231.0,186.0,82.0 \
-overlay.intensity 0.2,1 \
-overlay.threshold_min 0.2 \
-overlay.threshold_max 1 \
-tractography.load /bcbl/home/home_g-m/lmengxing/TESTDATA/analysis-AL_07/sub-S038/ses-T01/output/AL25_clean.tck \
-tractography.lighting 1 \
-tractography.colour 231.0,186.0,82.0 \
-mode 3 -noannotations -fullscreen