minc_pretty_pic_m.pl

generate publication-quality montage images from MINC volumes

minc_pretty_pic_m.pl <input.mnc> <output_image> [options]

DESCRIPTION

minc_pretty_pic_m.pl is a variant of minc_pretty_pic.pl that generates multi-pane slice montage images with multiple slices per orientation. It produces a grid of slices spanning the volume, which is useful for reviewing the full extent of a brain volume or overlay in a single composite image.

The tool supports the same overlay, mask, LUT, RGB channel, and layout options as minc_pretty_pic.pl, but without title/font/adjust options. It is designed for generating comprehensive montage views.

OPTIONS

--verbose: Print progress information during processing.
--clobber: Overwrite existing output files.
--image-range <min> <max>: Set the display range for the primary input volume.
--ovl-range <min> <max>: Set the display range for the overlay volume.
--overlay <mnc>: Overlay the specified volume on top of the primary volume.
--mask <mnc>: Apply the specified mask to restrict the displayed region.
--scale <f>: Scale factor for the output image size.
--separate: Output each slice as a separate image file.
--coronal: Include coronal slices in the output.
--sagittal: Include sagittal slices in the output.
--axial: Include axial slices in the output.
--max: Use maximum intensity projection instead of single slices.
--over: Display overlay on top of the primary image.
--red: Map the primary volume to the red channel.
--green: Map the primary volume to the green channel.
--blue: Map the primary volume to the blue channel.
--vertical: Arrange panes vertically instead of horizontally.
--trim-x <n>: Trim the specified number of voxels from the x-axis borders.
--trim-y <n>: Trim the specified number of voxels from the y-axis borders.
--trim-z <n>: Trim the specified number of voxels from the z-axis borders.
--shift-x <n>: Shift the slice position along the x-axis.
--shift-y <n>: Shift the slice position along the y-axis.
--shift-z <n>: Shift the slice position along the z-axis.
--cyanred: Use a cyan-red diverging colour map for the overlay.
--lut <file>: Apply the specified look-up table file to the primary volume.
--discrete: Treat the LUT as a discrete (label) colour map.
--background <color>: Set the background colour of the output image.
--foreground <color>: Set the foreground (text) colour of the output image.
--noresample: Do not resample the input volume before slice extraction.
--tile <cols>x<rows>: Arrange slices in a tile grid with the specified columns and rows.
--geo <WxH>: Set the output image geometry (width x height in pixels).
--compact: Remove spacing between panes for a compact layout.
--debug: Print additional debugging information.

EXAMPLES

Generate an axial montage through the whole brain:

minc_pretty_pic_m.pl --axial subject_t1.mnc montage.png

Generate a montage with an overlay and custom display range:

minc_pretty_pic_m.pl --overlay labels.mnc --lut spectral.lut \
    --discrete --image-range 0 100 \
    subject_t1.mnc montage.png

Generate a compact coronal montage:

minc_pretty_pic_m.pl --coronal --compact --clobber \
    subject_t1.mnc coronal_montage.png

AUTHOR

Vladimir S. Fonov. McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS