comqa - Simple fMRI stability test

Command line program to analyse dynamic series of a phantom, find and track any changes in the position of the centre of mass of the phantom (assuming the phantom is spanned in all three dimensions) and calculate mean and standard deviation of intensities values in a spherical region of interest centred on the COM. Results are written to both text and CSV files. COM values are in units of voxels (be aware of this if the input Analyze file has non-isotropic voxels, resulting in a non-spherical ROI in real units).

comqa [-d] [-rad n] [-ct] [-tsnr] [-acr] [Analyze/NIFTI filename] [-p phase image filename]

If no command line options are entered, the program just requests the multivolume input Analyze filename. Optional command line flags may be specified -

-d

Outputs extra diagnostic information for debugging.

-rad n

Overrides the default radius of the spherical ROI by n pixels. If n is negative, then set the radius automatically (currently 10% of the matrix size). Whether this flag is specified or not, the value of the radius used is output, in pixels.

-ct

Assumes the input images are from a CT scan rather than MRI. In the MR images, the edge of the object is the liquid/plastic boundary, whereas in CT images both the liquid and the plastic are visualised, which means different phantom diameters will be measured depending on modality. This option thresholds the CT image to around -20 HU so that the FWHM used to calculate the phantom diameters should find the water/plastic boundary rather than the plastic/air boundary.
Any objects with similar intensities (e.g., couch, or head holder) may need to be removed from the CT images prior to running this program.

-tsnr

Also calculate and save temporal SNR images.

-acr

Assuming the images are of the large ACR phantom, performs some basic calculations on slice 7 of 5.Image Intensity Uniformity and 6.Percent Signal Ghosting. The other values in the results file should not be used.