Hi Longchuan,

1) If you want tracts to stop at your cortical mask, you should use it as both the target and a stop mask. The waypoint mask you describe is probably unnecessary. If you want, you can track symmetrically by treating each mask as a seed and a target/stop mask, and then adding the results together.

2) It seems that the most straightforward way to measure this is to just use the number in the waypoints file (the number of samples that went from seed to target).

Peace,

Matt.

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Longchuan Li
Sent: Friday, August 29, 2008 2:27 PM
To: [log in to unmask]
Subject: [FSL] Visualize tracts that only reached the cortical target masks

Dear FSL users

I am looking at the corticospinal tracts from midbrain to precentral gyri. What I did were as follows: I first drew a seed mask at the cross section of corticospinal tracts at the level of pons. Then, I drew cortical masks at the precentral gyri. There is also a waypoint mask at the posterior part of internal capsules between these two masks.

My questions are:

1) How can I visualize the tracts that *only* reached the precentral gyri cortical masks? I was trying to use the cortical masks as the waypoint masks as well as target masks but only found some of the tracts were passing though them, not showing what I want to see. I am also thinking to use the cortical masks as the seed mask and use the corticospinal mask (original seed mask) as the target mask to track the tracts. But I think I need advice from experts before I do them in batch.

2) Is the total number saved in "seed_to_mycorticalmasks.nii.gz" (extracted by using the mean of the total * number of voxels) a good way to quantify the strength of the paths between my seed mask and cortical target masks?

Thank you

Longchuan Li