Future updates

Note

Any update ideas can be given here: https://github.com/elliohow/fMRI_ROI_Analysis_Tool/discussions

General

  • Test fRAT with empty parameters for cases where a single metric is set to be reported and not a comparison between multiple parameters - May need to find references to config.parameter_dict/cfg.parameter_dict to see how it is handled when blank

  • Summarise data across an ROI (time series analysis)

  • Add support for custom statistical map functions

  • Add option to only keep essential files when running statistical map functions (such as ‘_tSNR’)

  • To facilitate easier testing of new features during development, add ability to test only ROI analysis, only statistical map creation, or both.

  • Dash barchart code needs an overhaul as it isn’t currently viable to easily add new features

    • Long names currently get cutoff

  • Give user ability to find fRAT version

  • Print log of terminal output. This will allow the user to track where fRAT terminated in the case of a crash

  • Save path of last analysed folder so its easier to string together statmap creation and ROI analysis

  • Separation of noise volumes currently returns false positives

  • Add option to use atlases with the 25 or 50 probability threshold

  • (Potential) Add ability to analyse more than fMRI volumes (such as anatomical volumes)

  • (Potential) Add easy way load analysis results data so jupyter notebook can be used to explore the data with graphs/statistics

GUI

  • Separate fRAT into 3 components (main analysis, creation of statmaps such as tSNR, general fMRI tools)

  • Ability to make saveable analysis profiles to quickly swap between settings

    • Need to also add ability to keep toml files up to date if any new options have been added/removed

  • Increase linux compatibility

Analysis

  • Add option to bootstrap confidence intervals

  • Allow registration to more templates (such as http://ccraddock.github.io/cluster_roi/)

  • Allow registration to custom templates and ROI atlases

  • Add ability to skip running a file through analysis if file has already been ran through analysis

    • May be good for combining large datasets or adding new participants to the analysis

    • May only be possible with participant averaged data

    • Currently output folder is deleted when rerunning analysis due to mcf files

    • Need to find a way to deal with files which have now been set to ignore in paramValues.csv

    • Need to also force the analysis to rerun if parameter values have changed

  • Increase clarity of output files

  • fRAT should check paramValues.csv before running anatomical file alignment to see if any subjects can be skipped

Figures

  • 3d representation of the brain grid data

  • Option to use scientific notation for brain figures: https://github.com/nilearn/nilearn/issues/2220

  • Ability to add manual lines to graphs (for example, to represent minimum usable tSNR)

  • Improve customisation options of figures (for example, currently barcharts look too big if fewer parameters selected)

  • Add option to add number of voxels to histogram plots

  • Give one IV barcharts colour

  • Implement mixed-roi scaled brain figures

  • Add option to underlay MNI template under each brain grid image

  • (Potential) Interactive plots

Statistics

  • Add ability to compare if linear mixed model coefficients significantly vary between regions

  • Add figures and testing for linear mixed model assumptions (linearity, normality and homogeneity)

  • Add \(r^{2}\) statistics to t-tests

Statmaps

  • Handle the func_preprocessed folder more elegantly, currently it is replaced each time statmaps are created

Known issues

  • Coefficient map creation during statistics step can fail with interaction effects if the the IV’s contain an

independent variable.