MotorMEICAModeling

Testing aggressive, moderate, and conservative methods of implementing rejected ME-ICA components in subject-level motor-task analysis.

1. Motor calculations

FDcorrCalc.m: Function to calculate average FD and correlations of motion regressors with task regressor(s)

RUN_FDcorrCalc_Example.m: Example script to call FDcorrCalc.m for every dataset in a study

2. tedana

x.tedana_extReg.sh: Example script to create the required inputs and run tedana with external regressors

demo_external_regressors_motion_task_models.json: Tedana automatic classification decision tree to use (included as part of tedana v24.0.2)

3. Subject-level GLM

x.PreProc_RejectedICA.sh: Function to prep rejected ICA components w/ or w/o considering task-correlation and w/o or w/o orthogonalization based on the model used (Basic, ConsOrth, TaskCorr)

x.GLM_REML_ICA.sh: Function to run subject-level GLM including motion, motion derivatives, CO2, and 1 or 2 task regressors

x.RUN_GLM_Example.sh: Example script to run the above two functions

4. Group-level analysis

x.3dMEMA_1samp_Example.sh: Example script to run 3dMEMA

x.Cluster_Example.sh: Example script to run cluster simulation and creation of cortex and cerebellum ROIs based on results

5. Subject-level metrics

harvardoxford-cortical_prob_Precentral_Gyrus_2mm.nii.gz: Mask of precentral gyrus from Harvard-Oxford atlas, resampled to 2mm MNI space; for use in creating a mask to calculate metrics within

mni_prob_Cerebellum_p50_2mm.nii.gz Mask of cerebellum, thresholded at 50% probability and resampled to 2mm MNI space; for use in creating masks / ROIs

x.tSNR_calc.sh: Function to calculate mean and median tSNR within a mask

x.tstat_calc.sh: Function to calculate mean and median tSNR within a mask

x.activation_calc.sh: Function to calculate mean and median beta coefficient and percent activated voxels within a mask

x.spatialCorr_calc.sh: Function to calculate spatial correlation between beta coefficient maps from two runs, within a mask

x.dice_calc.sh: Function to calculate Dice coefficient between thresholded t-statistic maps from two runs, within a mask. Must have previously run x.activation_calc.sh to create the thresholded maps

x.RUN_Metrics_Example.sh: Example script to run the above three functions for every dataset in a study and save outputs to text files