[Mrtrix-discussion] Human Connectome Project dataset issue

[Parker, Christopher]

Hi Ivan and Mrtrix users,

I have just experienced the same problem with streamtrack SD_PROB. It does not produce any streamlines and hangs although still uses a lot of CPU. I think it might have something to do with the SH harmonic coefficient file (source argument in streamtrack), since when I use a harmonic coefficient file from a different scan it works fine (all other arguments were the same files). I need to find a solution to this also.

Best,
Chris
________________________________
From: mrtrix-discussion-bounces at www.nitrc.org [mrtrix-discussion-bounces at www.nitrc.org] on behalf of Ivan Alvarez [ivan.alvarez.11 at ucl.ac.uk]
Sent: 09 January 2013 15:03
To: mrtrix-discussion at www.nitrc.org
Subject: [Mrtrix-discussion] Human Connectome Project dataset issue

Hello Mrtrix users,

I tried analysing a sample subject from the recently available Human Connectome Project dataset (https://db.humanconnectome.org), and encountered an issue with CSD tractography in Mrtrix. In brief, the dataset has 1.25 mm isotropic voxels, 270 directions, 3 b-shells (1000,2000,300) and 2 repeats.

The tensor estimation worked fine, and am able to compute sensible-looking FA maps. The mask erosion is also fine, but when I view the response function coefficient, it displays an unusual shape (RCF<http://postimage.org/image/cl7tpwc3p/>). The csdeconv command returns no errors and the orientation plot looks reasonable. My problem is, when I attempt to perform tractography with the streamtrack command, the program hangs.

Any idea as to why this might be?

--
Kind regards,
Ivan Alvarez

PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH
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