Orientation:('R', 'A', 'S')
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413.12.1.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413EPI.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413.12.1.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413EPI.nii.gz
bet /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413EPIBet.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_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz -mas /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413EPIBet_mask.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413BET.nii.gz
fslsplit /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz GV_T3_1_1_1_4_20181126_102413 -z
For all slices ... 
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130000.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130000.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130001.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130001.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130002.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130002.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130003.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130003.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130004.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130004.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130005.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130005.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130006.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130006.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130007.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130007.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130008.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130008.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130009.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130009.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130010.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130010.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130011.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130011.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130012.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130012.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130013.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130013.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130014.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130014.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130015.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130015.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130016.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130016.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130017.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130017.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130018.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130018.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_1_1_1_4_20181126_1024130019.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130019.nii.gz -plots
fslmerge -z /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413_mcf.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130000.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130001.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130002.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130003.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130004.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130005.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130006.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130007.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130008.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130009.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130010.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130011.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130012.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130013.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130014.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130015.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130016.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130017.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130018.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_mcf/GV_T3_1_1_1_4_20181126_102413_mcf.mat/GV_T3_1_1_1_4_20181126_1024130019.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413_mcf.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413_mcfEPI.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413_mcf.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_1_1_1_4_20181126_102413/fMRI/rs-fMRI_niiData/GV_T3_1_1_1_4_20181126_102413_mcfEPI.nii.gz
Copy related physio data /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/Physio/GV_T3_1_1_1_4_20181126_102413/GV_T3_1_1_1_4_20181126_102413.PHYSWAV.12.I32 to rawMoData
avg. Respiration Rate: 109.07306763285024 1/min
avg. Card Rate: 424.5923913043478 1/min
Number of Repititions: 105.0