Modifying QC Generation - McIntosh-Lab/tvb-ukbb GitHub Wiki
Analyses generated by the QC Report can be modified to better suit your dataset; users may alter brightness, contrast, colormaps, ranges of slices, and specific NIfTI files being depicted in each QC image.
We do not currently provide a tool for users to add new analyses or overlay images to the QC Report. If you have any suggestions for analyses to be included in the QC Report, please let us know in the Discussions Page.
There are three types of overlay images featured in the QC Report: 1) lightbox 2) orthographic appended 3) edges. These overlay images are generated in tvb-ukbb/tvb_bb_QC/tvb_bb_QC.sh and may be customized with optional arguments described below.
Lightbox overlays features two images, one or more on top (overlays) and one on the bottom (underlay). This generates three images, one from each orientation.
Lightbox overlays are generated with tvb-ukbb/tvb_bb_QC/lightbox.sh.
-o <overlay_filepath> full filepath to overlay image
-p <overlay_cmap> fsl colourmap for overlay
-a <overlay_alpha_value> float from 0 to 100 for opacity of overlay
-j <overlay_type> overlay type (e.g. "label", "volume", "linevector")
-s <second_overlay_filepath> full filepath to second overlay image
-h <second_overlay_cmap> fsl colourmap for second overlay
-i <second_overlay_alpha_value> float from 0 to 100 for opacity of second overlay
-k <second_overlay_type> second overlay type (e.g. "label", "volume", "linevector")
-b <underlay_brightness> float from 0 to 100 for underlay brightness
-c <underlay_contrast> float from 0 to 100 for underlay contrast
-x <x_limit> int % of image to remove bilaterally in the x-axis (e.g. 10 removes 10% from each side)
-y <y_limit> int % of image to remove bilaterally in the y-axis (e.g. 10 removes 10% from each side)
-z <z_limit> int % of image to remove bilaterally in the y-axis (e.g. 10 removes 10% from each side)
Orthographic appended images provide the same type of overlay as Lightbox images, but with the the option to generate zoomed-in image overlays. This is particularly useful for analyzing the subcortex. This generates three images, one from each orientation.
Orthographic appended images are generated with tvb-ukbb/tvb_bb_QC/ortho_appended.sh.
-o <overlay_filepath> full filepath to overlay image
-p <overlay_cmap> fsl colourmap for overlay
-a <overlay_alpha_value> float from 0 to 100 for opacity of overlay
-j <overlay_type> overlay type (e.g. "label", "volume", "linevector")
-s <second_overlay_filepath> full filepath to second overlay image
-h <second_overlay_cmap> fsl colourmap for second overlay
-i <second_overlay_alpha_value> float from 0 to 100 for opacity of second overlay
-k <second_overlay_type> second overlay type (e.g. "label", "volume", "linevector")
-t <underlay_type> underlay type (e.g. "label", "volume", "linevector")
-b <underlay_brightness> float from 0 to 100 for underlay brightness
-c <underlay_contrast> float from 0 to 100 for underlay contrast
-x <x_limit> int % of image to remove bilaterally in the x-axis (e.g. 10 removes 10% from each side)
-y <y_limit> int % of image to remove bilaterally in the y-axis (e.g. 10 removes 10% from each side)
-z <z_limit> int % of image to remove bilaterally in the y-axis (e.g. 10 removes 10% from each side)
-X <x_zoom> float for x-axis zoom
-Y <y_zoom> float for y-axis zoom
-Z <z_zoom> float for z-axis zoom
-u <x_centre> float coordinates for centre of x-axis image (e.g. "0.05045 -0.11195")
-v <y_centre> float coordinates for centre of x-axis image (e.g. "0.05045 -0.11195")
-w <z_centre> float coordinates for centre of x-axis image (e.g. "0.05045 -0.11195")
-O <orientation> int (0,1,2) to generate only one image from one orientation instead of default three images of three orientations (0 - saggital, 1 - coronal, 2 - axial)
Edge images are also similar to Lightbox images, but with the overlaid image rendered as red lines. Edge images allow viewers to compare the alignment of prominent features. This is particularly useful for assessing registration quality. This generates six images, two from each orientation (underlay and overlay are switched between these two).
Edge images are generated with tvb-ukbb/tvb_bb_QC/edges.sh.
-s <standard_path> full file-path to folder containing standard images (e.g. ${FSLDIR}/data/standard). only use if one of the images to be overlaid is a standard image. if this option argument is used, then the first non-option argument must be the filename of a standard with a leading forward-slash (e.g. /MNI152_T1_1mm.nii.gz)
-l <limit> int % of image to remove bilaterally in all axes (e.g. 10 removes 10% from each side, for each axis)