Questions about a custom bundle

[htakemur]

Hello @arokem

I follow your suggestions to read the tutorial below to calculate the tract profile for custom bundles.
https://github.com/dipy/dipy/blob/master/doc/examples/afq_tract_profiles.py

It looks like the following part of the code handle orientation of fiber tract consistent across subjects, based on comparison with known fiber tract orientation.

model_arc_l_file, model_cst_l_file = get_two_hcp842_bundles()

model_arc_l = load_trk(
model_arc_l_file, reference="same", bbox_valid_check=False
).streamlines
model_cst_l = load_trk(
model_cst_l_file, reference="same", bbox_valid_check=False
).streamlines

feature = ResampleFeature(nb_points=100)
metric = AveragePointwiseEuclideanMetric(feature)

qb = QuickBundles(threshold=np.inf, metric=metric)

cluster_cst_l = qb.cluster(model_cst_l)
standard_cst_l = cluster_cst_l.centroids[0]

cluster_af_l = qb.cluster(model_arc_l)
standard_af_l = cluster_af_l.centroids[0]

oriented_cst_l = dts.orient_by_streamline(cst_l, standard_cst_l)
oriented_arc_l = dts.orient_by_streamline(arc_l, standard_af_l)

However, if the bundle is not included in these widely studied bundles, do you have any suggestions on how to ensure the consistency of orientation of fiber tracts across subjects (to avoid that tract profile direction is not flipped across subjects)?

[arokem]

Hi! That is indeed a challenge. One option I can think of is to use one subject as a "template" subject, using their bundles for the clustering and then using their centroids as the streamline according to which all the other subjects streamlines get oriented. You might want to play around with this a bit, for example to make sure that the bundles are oriented the same way in both hemispheres. Depending on the length of the bundle and its location in the brain, that might work well for all subjects. You'd probably want to check this, e.g., by plotting the node indices along the length of the bundle. See also this neurostars post for a couple of examples, and some code to do this: https://neurostars.org/t/putting-mrtrix-tractography-into-pyafq/26780/7?u=ariel_rokem.

[36000]

This function could be useful:

pyAFQ/AFQ/recognition/utils.py

Line 91 in fe30b28

def orient_by_streamline(sls, template_sl):

[htakemur]

@arokem @36000 Thank you very much for your response! I will try to follow what you suggest and contact back to you in this thread.