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Group analysis

To facilitate group analysis, PRESTUS automatically outputs key results as Nifti images in MNI space. Projection to MNI space can be done either using SimNIBS’ subject2mni command, or in MATLAB by reading in MNI2conform_12DOF.txt.

create_group_MNI_plots

Rationale

  • This will ensure that all figures will use the same scale
  • Allows one to add a ROI MNI mask to visualise targeting accuracy
  • Adds additional columns to each csv with information about intensity in the ROI mask, percentage of fwhm voxels within ROI etc.
  • When using structural MRI's, it also allows one to normalise the brightness so the discrepancy in average brightness between individual T1's is reduced.

Necessary input:

  • subject_list: list of all subjects that you want to include in the figures.
  • parameters: load the '.yaml' file using 'load_parameters.m' just as you would do in a pipeline.
  • options: a structure similar to 'parameters'. Most of these are (as the name would suggest) optional. only one of the two following parameters needs to be selected:
    • options.slice_to_plot = 0 (give the number of the slice)
    • options.plot_max_intensity = 0 (turn on by changing to 1)

Plotting a ROI mask

  • Use a mask saved in MNI space
  • Load it into the function under the option 'ROI_MNI_mask'
Optional parameters:
options.ROI_MNI_mask (:,:,:) # Loads in a 3d matrix of your ROI mask (in MNI space)
options.slice_label = 'y' # Selects the axis along which your slice is made
options.rotation = 90;  # Rotates your structural background figure
options.plot_heating = 1 # Binary option to enable or disable heating plots
options.outputs_suffix = '' # Allows you to add a string at the end of the name of your output to say, differentiate between plots of maximum intensity and a given slice
options.isppa_thresholds = [] # Manually set the Ipa range that is to be plotted
options.add_FWHM_boundary = 0 # Binary option to add a dotted boundary around the FWHM of intensity
options.add_ROI_boundary = 1 # Binary option to add a red boundary around your ROI mask
options.skip_missing = 0 # Binary option to skip subjects with missing files
options.brightness_correction = 0 # Binary option to normalise the brightness between structural T1's
options.average_target_brightness = 100 # Average targetted brightness, only used when brightness correction is enabled