Hello all,
I have been acquiring coronal 0.6 mm in-plane DTI scans of the hippocampus and surrounding cortex. I have been able to use FSL to calculate the tensors on this data and calculate my scalar maps (although FSL has trouble viewing the colormaps on this coronal data for some reason).
I would like to do probabilistic tractography to see if I can map the connectivity between two diffusion-space seed ROIs. I used bedpostx first and got all of the appropriate output files. Then I tried to apply probtrackx with a single mask (seed ROI) setting the termination zone to by another mask (target ROI). Everything runs fine, however my fdt_paths file essentially is identical to my seed mask file (except the value is equivalent to the number of samples I set, e.g. 1000). I've done this a few ways using the termination mask as a waypoint and the result is always the same.
I thought that perhaps since my voxel size is small, I should change the step size to something more appropriate (0.2), but I do have anisotropic slices (thickness = 3 mm). Not sure how to proceed.
Any thoughts you have on this would be greatly appreciated.
Thanks so much.
Best,
Mike
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Michael A. Yassa, Ph.D.
Assistant Professor in Psychological and Brain Sciences
Johns Hopkins School of Arts and Sciences
3400 N. Charles Street, Ames Hall
Baltimore, MD 21218
Tel: (410) 516-7055; Fax: (410) 516-4478
Email: [log in to unmask]
Web: http://pbs.jhu.edu/research/yassa/
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