process.log 14 KB

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  1. Orientation:('R', 'A', 'S')
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. For all slices ...
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. avg. Respiration Rate: 132.5719205834684 1/min
  33. avg. Card Rate: 427.72487844408425 1/min
  34. Number of Repititions: 105.0