[Mrtrix-discussion] Higher resolution TDI

[Thijs Dhollander]

Hi Mchandra,

While I just started to type an answer, I noticed myself how you probably got confused about the arguments and options for the tracks2prob command.  I'm going to assume you have the latest 0.2.9 version of MRtrix.  I just noticed the online version of the documentation is outdated, and some important things about tracks2prob have changed since that version.  You should check out the documentation that came with your version in .../MRtrix/doc/commands/tracks2prob.html (where "..." is the folder you installed it to).

Some (random) info and answers:

(1) From the online version of the documentation, compared to the documentation that comes with 0.2.9: tracks2prob used to have 3 arguments (tracks, template, output), but now it only has 2 (tracks, output).  "-template" became an option instead of an argument.  BUT... it seems you still NEED to supply a template (as a "-template"), i.e. also in the case you want to do a higher resolution TDI-like operation.  This explains your "No error" errors (I once got the same ones until I discovered this fact).  When you do a higher resolution with the "-vox" option, you still need to specify the "-template" option.  The latter one is now only used as a "field of view", while the "-vox" option is used for the resolution.

(2) There used to be a "-count" option, to override the default calculation of fractions.  In 0.2.9, this is the other way around (!): now there is a "-fraction" option, while the default behaviour is the absolute count.  This explains your "unknown option "count"" error.

So fixed versions of both your commands would be:

(1) tracks2prob -template sometemplate.mif -vox 1 -fraction whole_brain_tracks.tck fraction_tracks.mif

(2) tracks2prob -template anat.img whole_brain_tracks.tck track_counts.mif

For "sometemplate.mif" in the first one, I guess you might want to use "anat.img".

One last warning for the higher resolution one: depending on how much memory your machine has, you might run out of it.  To circumvent this in some way, you can create a new template (from your previous template) using a combination of "mrconvert" and "mrtransform" (with the "-replace" option), that has a smaller "field of view" (for instance: half the brain, some slices, etc...).

Kind regards,

Thijs Dhollander
PhD Student

thijs.dhollander at uz.kuleuven.ac.be
tel. +32 16 34 90 37
gsm. +32 475 36 44 27

Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)
Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven | http://www.medicalimagingcenter.be

From: mrtrix-discussion-bounces at public.nitrc.org [mailto:mrtrix-discussion-bounces at public.nitrc.org] On Behalf Of mchandra pal
Sent: dinsdag 24 mei 2011 22:02
To: mrtrix-discussion at public.nitrc.org
Subject: [Mrtrix-discussion] Higher resolution TDI

Hi,
I have two queries.

In the discussion forum, it was previously suggested that super-resolution TDI images can be generated using "-vox" option in tracks2prob command.
I used the commeand    tracks2prob whole_brain_tracks.tck -vox 1 fraction_tracks.mif      to obtain TDI image with 1 mm X 1mm x 1mm spatial resolution.

It shows:
tracks2prob: creating new template image...   - ok
tracks2prob: error opening tracks data file "whole_brain_tracks.tck": No error
tracks2prob: error opening tracks data file "whole_brain_tracks.tck": No error

Also, when I tried to generate TDI image with the fibre count through each voxel using option 'count' (e.g. tracks2prob whole_brain_tracks.tck -count -template anat.img track_counts.mif), it shows
tracks2prob: unknown option "count".

Please kindly suggest the correct ways to write these commands.

-mc pal
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