[Mrtrix-discussion] Human Connectome Project dataset issue

[Donald Tournier]

Hi Chris & Ivan,

OK, I think there are a few issues to consider here. The first thing is to
figure out why the response function estimated for these data is not right.
Are you using just a single shell of the HARDI data, or are you simply
feeding all 3 shells to MRtrix? MRtrix is only designed to handle single
shell data, so if you're doing the latter, it's no surprise that it will
have issues. It may be possible to analyse these kinds of data in a future
version, but for now you should stick to single-shell HARDI, unfortunately.

As to why the tracking hangs: the most likely reason is that the program is
failing to find a suitable seed point. The procedure in MRtrix is to select
a random point and a random orientation, compute the FOD amplitude, and
start tracking if that amplitude is greater than the -init_cutoff threshold
(by default, 0.2). If your response function is incorrect, there is a good
chance that the scaling of the resulting FODs will also be off, giving you
smaller FODs than expected - in which case streamtrack will try in vain to
find a single suitable seed point/orientation, and appear to hang. To
verify this, you could try using a -cutoff value of zero to see if that at
least produces tracks. You could also use the find_SH_peaks command on the
CSD output file, and check the FOD peak amplitudes (although it's a little
more work to figure out how to extract the amplitude from that).

If none of this helps, I'm happy to have a look at the data - usually
quicker to troubleshoot that way...

Cheers,

Donald.


On 12 January 2013 02:49, Parker, Christopher <
christopher.parker.10 at ucl.ac.uk> wrote:

>  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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> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
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>
>


-- 
*Dr Jacques-Donald Tournier
*
Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg  Vic  3084
Ph:  +61 3 9035 7033
Fax:  +61 3 9035 7307
www.florey.edu.au
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