Daily Journal

12.05.2026

  • Initialized the main repository (see commit here)

14.05.2026

  • Initialized the report repository (see commit here)

15.05.2026

  • Welcome tour given by Masui san
  • CBI meeting
  • Created the main project website (see commit here)

18.05.2026

  • Updated the bibliography (see commits here)
  • Created the source page on the main project website (see commit here)
  • Meeting with Ayumu and Okito san
  • Went to Seika town hall to announce myself
  • Fixed an issue where the bibliography inside the report submodule wasn’t working on the main project website (see commit here)

19.05.2026

  • Started the Alizadeh 2025 paper summary (see commits here and here)
  • Updated the bibliography (see commits here and here)
  • Added daily journal page to main project website (see commit here)

20.05.2026

  • Added a flake.nix with uv to the project repository (see commit here)
  • Finished Alizadeh 2025 paper summary v1 (see commits here and here)
  • Created fuzzy fMRIPrep 25.2.5 Dockerfile (see commit here)

21.05.2026

  • Started the Andy’s Brain fMRIPrep tutorial
  • Troubleshooted an issue regarding the fuzzy fMRIPrep container and fMRIPrep runs
    • Found that without the --anat-only flag the run would crash at the skullstrip_first_pass step
  • Re read the Alizadeh 2025 paper summary to prepare for Monday meeting
  • Started setting up the ATR VPN

22.05.2026

  • Continued Andy’s Brain fMRIPrep tutorial
  • Fixed the fuzzy fMRIPrep skullstrip_first_pass issue (see commit here)
    • What made the step fail was that verificarlo was outputting logs to stderr
  • CBI meeting
  • Fixed typos and bugs in the Alizadeh 2025 paper summary (see commits here)
  • Updated the bibliography (see commit here)

25.05.2026

  • Gave a last read to the Alizadeh 2025 paper summary for today’s meeting
  • Meeting with Ayumu and Okito san
  • Requested access for docker rights on the cluster
  • Started writing slurm and local parallel computing scripts (see commit here)

26.05.2026

  • Troubleshooted the multiprocessing.Manager() issue
    • The Docker version was too old
  • Published Docker image to DockerHub (see here)
  • Continued the slurm fuzzy fmriprep script (see commit here)
  • Continued the parallel fmriprep script (see commit here)
  • Started the sequential_jobs script (see commit here)
  • Tried to make some reproduction runs on the cluster unsuccessfully

27.05.2026

  • Fixed the different run scripts (see commit here)
  • Tested the run scripts and made fMRIPrep parallel test runs on several nodes
  • Started the NPVR simulation notebook (see commit here and notebook here)

28.05.2026

  • Finished the v1.0.0 of the NPVR simulation notebook (see commits here and notebook here)
  • Added 2 utils nu script to get the subjects by common laboratory and their filename (see commits here)

29.05.2026

  • Wrote the necessary scripts to run the parallel_jobs.sh script with PBS (see commit here)
  • CBI meeting
  • Fixed the parallel_jobs.sh directory creation and added a step to pull the Docker image if not present (see commit here)
  • Modified the PBS run_parallel_jobs.sh script to add a metadata file creation and fixed the parallel jobs work directory name (see commit here)
  • Fixed the output filenames the get_sub_filename_by_common_lab.nu script (see commit here)
  • Fixed different issues in the pbs run_parallel_jobs.sh script (see commit here)
  • Ran 15 fMRIPrep runs on the cluster nodes

01.06.2026

  • Informed myself on the connectivity analysis pipeline
  • Began a connectivity analysis pipeline overview document (see commit here)
  • Meeting with Prof. Esteban
  • Opened an issue in the Numerical-Variability-of-functional-MRI-Graph-Measures repository (see here)
  • Added a github action to the report repository to automatically release the report (see commits here)
  • Add the Download Thesis menu button

02.06.2026

  • Started the fuzzy_fmriprep_graph_metrics_analysis marimo notebook (see commits here and notebook here)
    • Computed some FC matrices (currently very slow)

03.06.2026

  • Continued the fuzzy_fmriprep_graph_metrics_analysis notebook (see commits here and notebook here)
    • Changed the FC matrices computations to be in parallel
    • Added threshold graphs to the notebook
  • Started a first draft of the project Gantt diagram (see commit here and page here)

04.06.2026

  • Continued the fuzzy_fmriprep_graph_metrics_analysis notebook (see commits here and notebook here)
    • Computed graph metrics on the thresholded graphs
    • Computed and plotted NPVR
  • Contributed to the report thesis repository (see PR here)
  • Began the report cover page (see commits here)

05.06.2026

  • Made the fuzzy_fmriprep_graph_metrics_analysis notebook save some of it’s output (see commit here and output here)
    • FC matrices
    • Threshold graph plot
    • Graph metrics
    • NPVR variation plots
  • Ran several versions of the connectivity analysis pipeline (see commit here)
  • CBI meeting
  • Fixed a bibliography issue in the school template (see PR here)
  • Started the report abstract (see commit here)

08.06.2026

  • Continued the report abstract and acknowledgment (see commits here)
  • Fixed project python dependencies
  • Continued the fuzzy_fmriprep_graph_metrics_analysis notebook (see commits here and notebook here)
    • Added the NVPR per brain region plots
    • Fixed an issue in the calculate_npvr_data function
    • Added NPVR calculation details

09.06.2026

  • Continued the fuzzy_fmriprep_graph_metrics_analysis notebook (see commits here and notebook here)
    • Made the graph metric calculation run in parallel
    • Fixed the v1 run metadata
  • Added QOL to the fuzzy_fmriprep_graph_metrics_analysis notebook (see commit here)
  • Changed the Docker run command inside run_parallel_jobs.sh to add replicabiliy parameters (see commit here)
  • Meeting with Ayumu and Okito san

10.06.2026

  • Changed the Docker run command inside run_parallel_jobs.sh to add cifti output (see commit here)
  • Cleaned up the fuzzy_fmriprep_graph_metrics_analysis notebook (see commits here and notebook here)
    • Reversed the color of the threshold plots
    • Made the notebook reusable
    • Polished the overall code
    • Renamed the notebook
    • Changed the output paths
  • Started the fuzzy_fmriprep_fc_matrices_analysis notebook (see commit here and notebook here)

11.06.2026

  • Continued the fuzzy_fmriprep_fc_matrices_analysis notebook (see commits here and notebook here)
    • Added different plots from the previous FC matrices, as the current one are still running
  • Meeting with Prof. Esteban and Phd. Chatelain

12.06.2026

  • Looked into what to do with the FC matrices extraction MCA perturbation
  • Started re-reading this paper)
  • Wrote a small script to test OS numerical variability

15.06.2026

  • Started the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)
  • Contributed to the PCA dimensionality reduction github repository (see PR here)
    • Transformed the project into a Python package

16.06.2026

  • Continued the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)
    • Added the PCA feature plot for the wanted metrics
  • Contributed to the PCA dimensionality reduction github repository (see PR here)
    • Improved the PCA feature plot title and added x and y labels

17.06.2026

  • Continued the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)
    • Made the PCA feature extraction more modular
    • Started plotting the PCA FC MDD vs HC brains

18.06.2026

  • Continued the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)
    • Started analyzing the BMB dataset
  • Realized a mistake in the current fuzzy_pca_dim_reduction_analysis notebook analysis pipeline
    • I only plotted the FC that were unique between all the MDD vs HC PC instead of plotting all the FC of the selected PC

19.06.2026

  • Continued the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)
    • Corrected the analysis pipeline
    • Finished the first version of the notebook reproduction part.

22.06.2026

  • Finished the reproduction part of the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)
    • Fixed an issue where the parcellation regions were not the correct one
    • Fixed an issue with the FC matrices element indexes
    • Improved the FC brain plot

23.06.2026

  • Started the FC matrix extraction in the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)
    • Only added the basic pipeline until the extraction
  • Started reading the TS harmonization paper
  • Tried to create a fuzzy numpy docker container

24.06.2026

25.06.2026

  • Finished the regular FC matrices extraction part of the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)

26.06.2026

  • Fixed a mistake in the comparison of the extracted FC matrices and the harmonized ones in the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)
  • Started the harmonization procedure in the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)

29.06.2026

  • Continued the harmonization procedure in the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)
  • Installed a local LLM (this model and Cherry studio to help troubleshooting

30.06.2026

  • Looked into how the harmonization was done mathematically
  • Started a Excalidraw schema (see here
  • Continued the harmonization procedure in the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)

01.07.2026

  • Finished writing the code for the harmonization in the fuzzy_pca_dim_reduction_analysis notebook (see commits here and notebook here)
    • It still needs testing

02.07.2026

  • Fixed and verified the harmonization code in the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)

03.07.2026

  • Ran a first fuzzy PCA dimensionality reduction analysis on 2 runs, with the pipeline used for the reproduction (see commit here and notebook here)

06.07.2026

  • Ran 100 fuzzy PCA dimensionality reduction, made quite in depth analysis and started BMB extraction (see commits here)

07.07.2026

  • Created my Ai usage presentation slides (see slides here)
  • Finished gathering the BMB subjects and launched 2 fuzzy extraction runs

08.07.2026

  • Attended the AI usage workshop, and presented my view
  • Finished the BMB harmonization and started 10 new runs (see commits here)

09.07.2026

  • Updated the different README
  • Continued the BMB analysis (see commit here)
  • Cleaned the npvr_simulation notebook (see commit here)

10.07.2026

  • Updated the website home page (see commit here and page here)
  • Cleaned the different notebooks, README, etc… for the first submission (see commits here)

13.07.2026

  • Updated the fuzzy_pca_dim_reduction_analysis notebook via git lfs (see commits here and notebook here)
  • Updated sources + thesis title + home page gantt + report page (see commits here)
  • Scheduled a meeting with Okito and Ayumu san (tomorrow 11am)
  • Read several paper on MCA perturbations and data augmentation

14.07.2026

  • Meeting with Ayumu and Okito san
  • Tried to fix the images at the end of the fuzzy_pca_dim_reduction_analysis notebook not showing in the exported HTML file unsuccessfully

15.07.2026

  • Fixed the images issue in the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)
  • Started improving the numerical stability of the pca-based-feature-extraction Python package (see commits here)
  • Started updating the fuzzy_pca_dim_reduction_analysis notebook PC extraction with the more robust code (see commit here)

16.07.2026

  • Finished a first version of the pca-based-feature-extraction robust extraction (see commits here)
  • Ran the entire fuzzy_pca_dim_reduction_analysis notebook pipeline with the new PC extraction
  • Added Codebook to the different flake.nix

17.07.2026

  • Troubleshoot issues when running the complete fuzzy_pca_dim_reduction_analysis pipeline

21.07.2026

  • Finished fixing the complete fuzzy_pca_dim_reduction_analysis pipeline and ran the complete pipeline (see commit here)
  • Started the CBI presentation (see commits here and slides here)

22.07.2026

  • Continued the CBI presentation (see commit here and slides here)
  • Ran the old PC extraction (see commit here)
  • Modified the fuzzy_pca_dim_reduction_analysis plot_pcs functions to take as argument FC connections metric to plot (see commit here)

23.07.2026

  • Continued the CBI presentation (see commit here and slides here)
  • Added noise consensus plots + Added BMB regular FC matrix extraction + Added Fuzzy perturbations analysis (see commits here)

24.07.2026

  • Finished the CBI presentation slides (see commits here and slides here)
  • Presented my work at the CBI meeting

27.07.2026

  • Refined the report abstract and acknowledgment sections (see commits here and report here)
  • Added the select_perturbated_pca_features to pca-based-feature-extraction repository (see commits here)
  • Added the select_pca_features_single_precision to pca-based-feature-extraction repository (see commits here)
  • Added the select_pca_features_single_precision calculation to the fuzzy_pca_dim_reduction_analysis notebook (see commit here)

28.07.2026

  • Started the report introduction (see commit here)
  • Ran the perturbated FC plots and consensus (see commit here)

29.07.2026

  • Cleaned the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)

30.07.2026

  • Final cleaning of the fuzzy_pca_dim_reduction_analysis notebook (see commit here and notebook here)

01.08.2026

  • Fixed the index gantt diagram title (see commit here)

03.08.2026

  • Continued the report introduction, started the state of the art section and improved the abstract (see commit here)

04.08.2026

  • Continued the state of the art section (see commit here)
  • Started the development and methodology section (see commit here)

05.08.2026

  • Wrote the first version of the reproduction of Alizadeh et al., 2026 section (see commit here)

06.08.2026

  • Continued the methodology section (see commit here)

11.08.2026

  • Continued the methodology section (see commit here)
  • Started the result section (see commit here)

12.08.2026

  • Fixed calculate_npvr_difference in graph metrics notebook and added NPVR across brain regions (see commit here)
  • Fixed the global signal regression assessment in the project (see commit here)

13.08.2026

  • Fixed the global signal regression assessment in the project (see commit here)
  • Continued the result section (see commit here)
  • First draft of the report (see commit here)
  • Small cleanup of the website (see commit here)

14.08.2026

  • First draft of the executive summary (see commit here)
  • Changed wording in executive summary (see commit here)

15.08.2026

  • Updated poster figure DPI to 600 (see commit here)

16.08.2026

  • Rewrote the abstract (see commit here)
  • Corrected NPVR statistics in abstracts (see commit here)

17.08.2026

  • Updated template submodule (see commit here)
  • Changed wording about the global signal confound effect and upgraded abstract (see commit here)
  • Updated sources (see commit here)
  • Removed “bachelor thesis” from figure (see commit here)
  • Refined introduction wording and citation formatting throughout thesis (see commit here)
  • Added marek2018 reference and improved wording throughout thesis (see commit here)
  • Fixed upload workflow (see commit here)
  • Final cleaning of the report (see commit here)

18-27.08.2026

  • Made the final presentation slides and several rehearsals (see slides here)