Overview

Each map contains the number of times that voxel/vertex appears in the decomposition. This is then saved as a hitmap with each voxel/vertex containing the number of times a component value is in that voxel or as a binary mask to demonstrate coverage.

Output

Output depends on what imging files are present in the decomp directory. As a minimum (due to how nfact works) there will be a nii.gz file. However, depending on if the grey component is nii.gz/gii/.dscalar.nii this will depend on the output.

Prefix:

  • hitmap_*.nii.gz: Volume nii component. Components are not thresholded

  • hitmap_threshold*_.nii.gz: Volume nii component. Components are thresholded by zscoring to remove noise

  • mask_*.nii.gz: Volume nii component. Binary mask of unthresholded components

  • mask_threshold*.nii.gz: Volume nii component. Binary mask of thresholded components

  • *.gii: Surface gii component. Components are not thresholded

  • threshold_*.gii: Surface gii component. Components are thresholded by zscoring to remove noise

  • *.dscalar.nii: Cifti component, not thresholded

  • threshold_*.dscalar.nii: Cifti component. Components are thresholded by zscoring to remove noise

Note on output

If nfact_decomp has been run with thresholding then look at the _raw files as noise should have been filtered out. However, if not thresholding has been done at the decomp stage then look at the threshold images as this is a more accurate view of how many times a connectivity pattern at that vertex or voxel actually appears

Usage

nfact_Qc [-h] [-n NFACT_FOLDER] [-d DIM] [-a ALGO] [-t THRESHOLD] [-O]
NFACT QC options:
-h, --help

Show help message

-n, --nfact_folder

REQUIRED: Absolute path to nfact_decomp output folder. nfact_Qc folder is also saved within this folder.

-d, --dim

REQUIRED: Number of dimensions/components that was used to generate nfact_decomp image

-a, --algo

REQUIRED: Which algorithm to run qulatiy control on. Options are: NMF (default), or ICA.

-t, --threshold

Threshold value for z scoring the number of times a component comes up in a voxel in the image. Values below this z score are treated as noise and discarded in the non raw image.

-O, --overwrite

Overwite previous QC