onsemaple TFCE

gistfile1.sh

#merge maps - condition 1
fslmerge -t "/scr/adenauer1/workingdir/rs_analysis_group/main_workflow/merge_conn_maps_6_58_0/roi_6_58_0_masked_merged.nii.gz" /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13261.8d/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14390.d3/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14446.fb/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16090.c9/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12184.55/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15070.25/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14102.d1/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_09561.e0/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11944.79/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_07296.ec/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15403.c5/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15006.be/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12339.39/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14081.cb/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_18579.10/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12522.80/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_06222.f4/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13989.a7/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_06275.e0/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10080.62/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15466.cb/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15640.65/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12961.f8/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14388.48/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11109.5c/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13085.b0/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15475.c7/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14075.bd/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13565.7c/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10576.44/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_07070.79/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16101.0d/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_07346.36/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16758.c3/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_18094.87/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13630.5d/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13536.51/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_18758.73/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_09169.c5/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10581.e8/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14702.ea/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_18761.dc/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14018.65/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10960.82/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11111.28/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10439.86/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16939.4f/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16056.3d/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_19417.87/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16105.7a/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14074.a7/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_17421.31/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_19091.a3/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_17845.a2/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11059.75/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_09440.22/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14110.f4/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15890.ea/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11960.6a/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12315.9a/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii

# merge maps - condition 2
fslmerge -t "/scr/adenauer1/workingdir/rs_analysis_group/main_workflow/merge_conn_maps_-6_58_0/roi_-6_58_0_masked_merged.nii.gz" /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13261.8d/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14390.d3/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14446.fb/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16090.c9/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12184.55/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15070.25/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14102.d1/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_09561.e0/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11944.79/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_07296.ec/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15403.c5/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15006.be/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12339.39/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14081.cb/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_18579.10/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12522.80/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_06222.f4/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13989.a7/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_06275.e0/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10080.62/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15466.cb/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15640.65/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12961.f8/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14388.48/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11109.5c/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13085.b0/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15475.c7/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14075.bd/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13565.7c/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10576.44/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_07070.79/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16101.0d/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_07346.36/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16758.c3/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii 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/scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_18761.dc/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14018.65/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10960.82/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_11111.28/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_10439.86/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16939.4f/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16056.3d/_roi_-6.58.0/_fwhm_5/roi_-6_58_0_masked.nii 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#create difference map - cond 1 - cond 2
fslmaths "/scr/adenauer1/workingdir/rs_analysis_group/main_workflow/merge_conn_maps_6_58_0/roi_6_58_0_masked_merged.nii.gz" -sub "/scr/adenauer1/workingdir/rs_analysis_group/main_workflow/merge_conn_maps_-6_58_0/roi_-6_58_0_masked_merged.nii.gz" "/scr/adenauer1/workingdir/rs_analysis_group/main_workflow/diff_6_58_0_vs_-6_58_0/roi_6_58_0_masked_merged_maths.nii.gz"

#test cond 1 - cond 2
randomise -i "/scr/adenauer1/workingdir/rs_analysis_group/main_workflow/diff_6_58_0_vs_-6_58_0/roi_6_58_0_masked_merged_maths.nii.gz" -o "_6_58_0_vs_-6_58_0" -m "/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain_mask.nii.gz" -1 -T

#repeate the two above steps for cond2 - cond1

#paper: http://www.sciencedirect.com/science/article/pii/S1053811908002978
#website: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise