A repository for the HCP reproducibility paper

To generate Figure 1, run:

python ./bin/code/provenance_graph.py

To generate Figure 2, run:

python3 ./bin/code/heatmap_plot.py

• Source file

To generate Figure 5, first, make sure you downloaded binarized images using git-lfs. Then run:

python bin/code/binarized_heatmap_img.py

We already created the folder of binarized images between segmentation results in CetOS6 vs. CentOS7 for all subjects. You can create the binarized image for each subject using the following commands:

fslmaths subj1_os6.nii.gz -sub subj1_os7.nii.gz subj1_diff.nii.gz
fslmaths subj1_diff.nii.gz -bin subj1_diff_bin.nii.gz

To generate Figure 6, run:

python3 bin/code/regions.py

We already created a CSV file containing all the Dice values between segmented regions for all subjects in CetOS6 vs. CentOS7. You can compute Dice values for each subject using the following command:

python ./bin/code/Dice_region_csv.py subj1_os6.nii.gz subj1_os7.nii.gz fs_seg_dice_accumulated_20sbj.csv

(You may edit paper.tex without generating the pdf if you don't manage to).

0. Install pdflatex and bibtex
1. Compile the document: pdflatex -shell-escape paper ; pdflatex -shell-escape paper (yes, twice).
2. Generate the bibliography: bibtex paper ; pdflatex -shell-escape paper (yes, once again).

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