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This standalone script can be used to create tractometry visualizations with along-tract colors and glass brain. It would very helpful to have this in DIPY for reporting tractometry results such as those from BUAN (@BramshQamar ).
Some functionalities built with FURY API are already indipy_horizon, such as
Visualizing streamline files;
Visualizing binary images with the --roi_images (glass brain given brain mask nifti files);
Plot along-tract metrics given .npy files (e.g. pvals.npy from BUAN containing 1D array or list of values for each segment). We could also add support for .txt files. The script currently creates assignment maps with same bundle, but the user could supply two streamline files, one to visualize and one to use as a reference for assignment maps as long as they are co-registered.
Generate colors from matplotlib colormaps, with custom value range (e.g. 0-1 for FA and 1-100 for segment number), and save the color bar to file. I still need to add a binary mode to show non-sig vs. sig results.
Load/save camera angles after users rotate the angle to generate consistent images. In the python script, I used the set_camera function in FURY (this would also be great to have in dipy_horizon). This function currently cannot save the zoom parameter so the output images contain lots of white space, can anyone advise?
dipy_horizon has the --buan, --buan_thr and --buan_highlight flags, but I'm not sure what they do or how to use them. Can any of the above functionalities be merged with these flags? Or to not overload the color-related flags in horizon, we could the move these flag into a new CLI for tractometry specific visualizations?
Thanks!
The text was updated successfully, but these errors were encountered:
This standalone script can be used to create tractometry visualizations with along-tract colors and glass brain. It would very helpful to have this in DIPY for reporting tractometry results such as those from BUAN (@BramshQamar ).
Some functionalities built with FURY API are already in
dipy_horizon
, such as--roi_images
(glass brain given brain mask nifti files);But we would also like to:
dipy_horizon
). This function currently cannot save the zoom parameter so the output images contain lots of white space, can anyone advise?dipy_horizon
has the--buan
,--buan_thr
and--buan_highlight
flags, but I'm not sure what they do or how to use them. Can any of the above functionalities be merged with these flags? Or to not overload the color-related flags in horizon, we could the move these flag into a new CLI for tractometry specific visualizations?Thanks!
The text was updated successfully, but these errors were encountered: