[Mrtrix-discussion] tck file format

[Donald Tournier]

Hi micdtiserver,

Can I  confirm that you're trying to load the tracks file with a simple
fread()? These files contain a text header of variable size, so this won't
work in general - although you'll get the byte alignment right 25% of the
time just by sheer luck. There are matlab functions included in the MRtrix
source download that you can use directly, in the 'matlab' folder. Try
these out, and if they don't work, I'll look into it.

Cheers,

Donald.


On 17 August 2012 15:34, dti mic <micdtiserver at gmail.com> wrote:

> Dear mrtrix,
>
> I run streamtrack on one data using DT_STEAM, SD_STREAM and SD_PROB
> options respectively. All 3 results look well (in accordance with
> anatomical knowledge). However, I have some questions about the format of
> the 3 output tck files.
>
> I tried to load these 3 tck files into matlab, using fread('float32').
>
> For the DT_STREAM one, the loading data looks fine, all positive value
> separated by NaN triplets (corresponding to coordinates along the tracks I
> assume?).
>
> But in the SD_STREAM and SD_PROB tck files, fread('float32') return a lot
> of negative values ( I thought they all should be positive?), separated by
> non-NaN but extremely small numbers.
>
> I am wondering if I am doing something wrong here? Or there is some
> different setting in tck file format from different tractography options?
>
> All I tried to get is the coordinates along the tracks from tractography,
> like what I saw from DT_STREAM.
>
> Many thanks in advance!
>
> P.S.: Regarding to my previous issue with mrconvert fail in CentOS VBox, I
> have figured it out that it is due to some wired reasons: If the target
> file is located in my CentOS system hard drive (virtual), then the
> mrconvert works fine. However, if I put the target file in the shared
> folder (shared from my iMac), the command will fail. And it is not just
> mrconvert, but any other commands that call the mmap. I guess it has
> something to do with my VBox or my iMac. But anyway, it is not a problem
> for now.
>
> micdtiserver
>
>
>
>
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20120817/b69dc576/attachment.html