[ENH] add methods section

[Remi-Gau]

closes #63

This is meant as a first rough step.

[Remi-Gau]

The content should adapt depending on the arguments passed to the CLI.

See example below.

---

These results were generated with
giga_connectome (version 0.4.2.dev9+ga57c4f7, https://giga-connectome.readthedocs.io/en/latest/)
using Nilearn (version 0.10.3.dev94+g2b1504b68.d20231213, RRID:SCR_001362)
and TemplateFlow (version 0.8.1).

The following steps were followed.

1. Created subject specific grey matter mask in MNI space (MNI152NLin2009cAsym).

2. Sampled the Schaefer20187Networks atlas to the space of subject specific grey matter mask in MNI space.

3. Calculated the conjunction of the customised grey matter mask and resampled atlas to find valid parcels.

4. Used the new input specific grey matter mask and atlas to extract time series and connectomes for each subject.
   The time series data were denoised as follow:

   • Time series extractions through label or map maskers are performed on the denoised nifti file.
   • Denoising steps were performed on the voxel level:
     • spatial smoothing (FWHM: 5.0 mm)
     • detrending, only if high pass filter was not applied through confounds
     • regressing out confounds (using a simple strategy)
     • standardized (using zscore)
   • Extracted time series from atlas
   • Computed correlation matrix

5. Calculate intranetwork correlation of each parcel. The values replace the diagonal of the connectomes.

6. Create a group average connectome.

[codecov-commenter]

Codecov Report

Merging #77 (d2a4fad) into main (35e9756) will increase coverage by 0.31%.
Report is 3 commits behind head on main.
The diff coverage is 100.00%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #77      +/-   ##
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+ Coverage   91.31%   91.63%   +0.31%     
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  Files           9       10       +1     
  Lines         449      466      +17     
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+ Hits          410      427      +17     
  Misses         39       39              

Files	Coverage Δ
giga_connectome/methods.py	100.00% <100.00%> (ø)
giga_connectome/workflow.py	100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

[Remi-Gau]

Probably worth checking with COBIDAS and the bids BEP for connectivity to see what else can go in there.

What are the typical things you would expect to see in a methods section @htwangtw ?

[htwangtw]

1. post processing details done on fMRIPrep output
2. Atlas used
3. Connectome calculation methods (most common one is pearson's correlation with LedoitWolf covariance estimator)

[Remi-Gau]

For the atlas I can only have the name with have in the json files.
If those have more details then we could inject it in the methods. Probably worth waiting with the BIDS effort to standardize atlases to make a move there.

[htwangtw]

+1 for waiting on BIDS effort.
What you have here is more than sufficient comparing to what I have seen in papers

[htwangtw]

thank you this is a nice addition

[htwangtw]

+1 for waiting on BIDS effort.
What you have here is more than sufficient comparing to what I have seen in papers