cmind.pipeline.cmind_DWI_TRK_to_3plane

Functions

cmind_DWI_TRK_to_3plane(trackfile, ...[, ...]) Use the command line version of TrackVis, FSL & ImageMagick tools to generate 3-plane Tractography images
cmind.pipeline.cmind_DWI_TRK_to_3plane.cmind_DWI_TRK_to_3plane(trackfile, output_image_prefix, track_lengths=40, add_length_label=True, figure_title=None, image_scale_pct=50, extra_options='--no_annotation', stack_length_images=True, remove_intermediate_images=True, ForceUpdate=False, verbose=False, logger=None)[source]

Use the command line version of TrackVis, FSL & ImageMagick tools to generate 3-plane Tractography images

Parameters:

trackfile : str

filename of the .trk file to plot

output_image_prefix : str

full path of the output image, minus the image extension

track_lengths : int, optional

only display tracks > track_length. If this is a list, generate separate plots for each length in the list

add_length_label : bool, optional

If true, the left margin of the image will contain text annotating the lengths

figure_title : str, optional

Title to put at top of image

image_scale_pct : int, optional

rescale the rendered images by this amount before making the 3-plane image

extra_options : str, optional

string containing extra options to be passed on to track_vis. (see track_vis –help. e.g. –do_not_render to disable rendering to screen)

stack_length_images : bool, optional

If this is true, stack the images corresponding to each length vertically into a single image

remove_intermediate_images : bool, optional

If this is true, any intermediate images will be removed and only the final stacked image will be generated.

ForceUpdate : bool,optional

if True, rerun and overwrite any previously existing results

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

all_output_images : list

list of images generated