Orientation:('R', 'A', 'S')
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549.6.1.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549EPI.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549.6.1.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549EPI.nii.gz
bet /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549EPIBet.nii.gz -f 0.35 -m -r 45 -R -g 0.10
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz -mas /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549EPIBet_mask.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549BET.nii.gz
fslsplit /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz GV_T3_2_2_1_3_20181126_134549 -z
For all slices ... 
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490000.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490000.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490001.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490001.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490002.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490002.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490003.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490003.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490004.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490004.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490005.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490005.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490006.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490006.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490007.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490007.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490008.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490008.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490009.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490009.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490010.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490010.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490011.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490011.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490012.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490012.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490013.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490013.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490014.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490014.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490015.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490015.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490016.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490016.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490017.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490017.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490018.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490018.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_2_2_1_3_20181126_1345490019.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490019.nii.gz -plots
fslmerge -z /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549_mcf.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490000.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490001.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490002.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490003.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490004.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490005.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490006.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490007.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490008.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490009.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490010.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490011.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490012.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490013.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490014.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490015.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490016.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490017.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490018.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_mcf/GV_T3_2_2_1_3_20181126_134549_mcf.mat/GV_T3_2_2_1_3_20181126_1345490019.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549_mcf.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549_mcfEPI.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549_mcf.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_2_2_1_3_20181126_134549/fMRI/rs-fMRI_niiData/GV_T3_2_2_1_3_20181126_134549_mcfEPI.nii.gz
Copy related physio data /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/Physio/GV_T3_2_2_1_3_20181126_134549/GV_T3_2_2_1_3_20181126_134549.PHYSWAV.6.I32 to rawMoData
avg. Respiration Rate: 75.15182186234819 1/min
avg. Card Rate: 412.5759109311741 1/min
Number of Repititions: 105.0