ASL Corrections Tab

Corrections are changes made to the input data before the model fitting is performed. currently four possible sources of corrections are supported:

Motion correction

If enabled this will apply motion correction to the ASL data set using the FSL MCFLIRT tool.

If you prefer, you can do motion correction independently within Quantiphyse (or elsewhere) and disable this option in the ASL processing.

ENABLE volume selection

This uses the ENABLE method to remove ‘bad’ volumes from the cASL data to improve overall quality. This can be useful if there are a small number of volumes with, for example, major motion artifacts.

When selected, an additional tab appears headed ENABLE:

ENABLE options

Minimum number of repeats per time point

ENABLE will always leave at least this many repeats of each TI/PLD, so for example if you start out with 8 repeats of each TI/PLD you may end up with 7 repeats of the first TI, 4 of the second, etc. But you will never get just 2 repeats preserved for a TI.

Custom grey matter ROI

ENABLE bases its quality measures on signal-noise ratio in grey matter. If you already have a grey matter ROI for your data you can specify it here. Otherwise ENABLE will use the segmentation of the structural data you provide on the Structural Data tab.

Custom noise ROI

This is an ROI which defines a part of your data to be used to estimate the noise. If you don’t specify anything ENABLE will invert the brain mask and use that, which is normally a reasonable choice.

ENABLE Quality measures

The table of quality measures is filled in after ENABLE has run and provides a summary of which volumes in your data were kept and which were removed.

Distortion correction

This corrects for the distortion of the image caused by field inhomogeneities. Two methods are provided: Fieldmap images or a phase-encode reversed (Blipped) calibration image.

Generic distortion correction options

Whichever method you select, you will need to select the phase encoding direction and the echo spacing.

The encoding direction is relative to the raw data axes which normally corresponds to scanner co-ordinates. However you should check the effect of distortion correction visually to ensure that the changes are in the axis that you expect.

The echo spacing is the true echo spacing (also known as dwell time) and should be specified in ms. The total readout time is this value multiplied by the number of slices (in the phase encoding direction) minus 1.

Distortion correction using fieldmap images

Three images must be provided - you must load them into Quantiphyse first. The first is the fieldmap itself, the second is the magnitude image and the third is the brain extracted version of the second.

Distortion correction using CBLIP images

The CBLIP image must be loaded into Quantiphyse and specified here.