Orientation:('R', 'A', 'S')
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245.5.1.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245EPI.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245.5.1.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245EPI.nii.gz
bet /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245EPIBet.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_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz -mas /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245EPIBet_mask.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245BET.nii.gz
fslsplit /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/fslScaleTemp.nii.gz GV_T3_6_2_1_3_20190211_122245 -z
For all slices ... 
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450000.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450000.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450001.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450001.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450002.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450002.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450003.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450003.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450004.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450004.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450005.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450005.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450006.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450006.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450007.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450007.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450008.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450008.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450009.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450009.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450010.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450010.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450011.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450011.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450012.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450012.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450013.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450013.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450014.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450014.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450015.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450015.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450016.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450016.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450017.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450017.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450018.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450018.nii.gz -plots
mcflirt -in /Users/pallastn/ImageProcessing/GIT/AIDAmri/bin/3.3_fMRIActivity/GV_T3_6_2_1_3_20190211_1222450019.nii.gz -out /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450019.nii.gz -plots
fslmerge -z /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245_mcf.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450000.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450001.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450002.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450003.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450004.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450005.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450006.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450007.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450008.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450009.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450010.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450011.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450012.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450013.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450014.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450015.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450016.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450017.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450018.nii.gz /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_mcf/GV_T3_6_2_1_3_20190211_122245_mcf.mat/GV_T3_6_2_1_3_20190211_1222450019.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245_mcf.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245_mcfEPI.nii.gz
fslmaths /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245_mcf.nii.gz -Tmean /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/GV_T3_6_2_1_3_20190211_122245/fMRI/rs-fMRI_niiData/GV_T3_6_2_1_3_20190211_122245_mcfEPI.nii.gz
Copy related physio data /Volumes/AG_Aswendt_Projects/TVA_GFAP_Vimentin_Göteborg/MRI/proc_data/P7/GFAP_Vim/Physio/GV_T3_6_2_1_3_20190211_122245/GV_T3_6_2_1_3_20190211_122245.PHYSWAV.5.I32 to rawMoData
avg. Respiration Rate: 132.5719205834684 1/min
avg. Card Rate: 427.72487844408425 1/min
Number of Repititions: 105.0