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https://github.com/carobellum/degenerationconnectivity

Code for analysing functional connectivity of cerebellar degeneration patients for manuscript Nettekoven et al., 2024.
https://github.com/carobellum/degenerationconnectivity

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Code for analysing functional connectivity of cerebellar degeneration patients for manuscript Nettekoven et al., 2024.

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# DegenerationConnectivity

Code for analysing functional connectivity of cerebellar degeneration patients for manuscript [Nettekoven et al., 2024](https://doi.org/10.1101/2024.07.05.602300).



## Dataset information

The data files available in this repository were derived from MRI scans of 40 patients diagnosed with pure cerebellar cortical degeneration and 40 age and sex-matched neurologically healthy individuals. All individuals participated a five-day motor training. On the days before and after training, participants underwent a structural MRI scan and a functional resting-state scan in addition to a motor assessment. 



![Schematic of motor training apparatus and study design schematic](img/study_protocol.png)



Functional data is missing for (subject, timepoint):

- sub-57, post

- sub-70, pre

- sub-70, post



Structural data was acquired from all subjects.



## Notebooks / Code to replicate different sections of the paper



Dependencies for all code sections: see ```requirements.txt``` (run pip install -r requirements to install all required packages into your environment)



### Study demographics

Study demographics, demographics for template generation and validation sample (Supplementary Table 1), and demographics for FIX training datasets

```notebooks/demographics.ipynb```



### Study-specific template

Fissure distances in template, SUIT and MNI space was calculated using:

```scripts/compare_fissures.py```



Fissure overlap was plotted (Fig 1B-D) and compared using:

```notebooks/stats_template.ipynb```



FIX performance with template registrations and standard registrations was plotted (Fig 1E) and evaluated using:

```notebooks/stats_fix.ipynb```



The study-specific template and associated files can be found in the [DegenerationControlTemplate](https://github.com/carobellum/DegenerationControlTemplate) repository.



### Connectivity



#### Extracting ROI timecourses



ROI timecourses were extracted from functional data in native space using:

```scripts/seed_ts.sh```



#### Correlating ROI timecourses



Functional connectivity between timecourses was calculated using:

```scripts/seed_corr.py```



#### Statistical analysis of functional connectivity

Data was loaded from dataframes, normalized and brought into the correct shape for analysis using:

```r/data_connectivity.R```



Baseline connectivity differences were plotted (Fig 3A & 3B) using:

```r/plots_connectivity.R```



Connectivity change was plotted (Fig 4, 5, 6 & 7) using:

```notebooks/plots_connectivity_change.ipynb```



Statistical tests on functional connectivity were calculated using:

```r/stats.R```



Model assumptions were tested using:

```r/model_assumptions.R```



Connectivity results were plotted using:

```r/plots_connectivity.R```