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ENH: implement the hierarchical clustering analysis of within-scanner SC reliability#560

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celprov wants to merge 24 commits intoTheAxonLab:mkdocsfrom
celprov:enh/within_scanner_sc_reliability
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ENH: implement the hierarchical clustering analysis of within-scanner SC reliability#560
celprov wants to merge 24 commits intoTheAxonLab:mkdocsfrom
celprov:enh/within_scanner_sc_reliability

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@celprov celprov commented Apr 10, 2026

I have implemented the analyses we promised under the section "hierarchical clustering analysis of within-scanner SC reliability" of our registered report.
For now, the code runs on simulated SC matrices or on the FC matrices loaded from HCPh.
Specifically, I implemented:

  1. aggregating the SC matrices in an array amenable for clustering analysis
  2. perform hierarchical clustering using Scikit-learn as pre-registered and plot the dendrogram
  3. extract average head motion, phase encoding direction, time of day, and room temperature to investigate whether such confounds explain similarity between SC matrices
  4. perform tSNE; the documentation of tSNE mention it is recommended to reduce dimensionality with PCA to approx 50 features if nbr of feature is too high (2016 in the case of the lowest DiFuMo scale), so we need implement this.
  5. Load the confounds and color the dendogram and the tSNE embedding according to factor values.

celprov added 24 commits June 5, 2025 11:39
…similarity/variability between SC matrices from different sessions
…y/variability between SC matrices from different sessions
…similarity/variability between SC matrices from different sessions
…e pre-registered that we would use scikit-learn, thus I implemented the clustering code similarly to how it is done in clustering the carpetplot in MRIQC
…king yet but anyway we need to wait to have the real SC matrices to correctly match the confounds value with SC matrices
…an reuse it across different analyses separated into different jupyter notebooks
…similarity/variability between SC matrices from different sessions
…y/variability between SC matrices from different sessions
…similarity/variability between SC matrices from different sessions
…e pre-registered that we would use scikit-learn, thus I implemented the clustering code similarly to how it is done in clustering the carpetplot in MRIQC
…king yet but anyway we need to wait to have the real SC matrices to correctly match the confounds value with SC matrices
…an reuse it across different analyses separated into different jupyter notebooks
…th SC matrices later)

enh: load confounds and plot the dendogram and tSNE results coloring by factor values
…v/hcph-sops into enh/within_scanner_sc_reliability
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