[Mrtrix-discussion] How to generate fibers that end near the GM

[Romascano David]

Hi everyone,

I'm trying to generate 100'000 fibers that start and end near the GM, and seeding randomly from the WM.

Following this post (www.nitrc.org/pipermail/mrtrix-discussion/2011-October/000289.html<http://www.nitrc.org/pipermail/mrtrix-discussion/2011-October/000289.html>), I manage to create tracks that connect the left thalamus with the left cortex for example, by running the following command:

streamtrack -seed WM_mask.nii -mask WM_mask.nii -include R_thalamus_mask.nii -include R_cortex_mask.nii -number 10000 -maxnum 100000 -minlength 10 -step 1 -nomaskinterp -stop SD_PROB FODsh.mif fibers.tck

I then tried to generate fibers that start and end near the GM. To filter tracks that end near the GM, I dilated my GM mask and set it twice as an inclusion ROI in the command:

streamtrack -seed WM_mask.nii -mask WM_mask.nii -include GM_dil_mask.nii -include GM_dil_mask.nii -number 10000 -maxnum 100000 -minlength 10 -step 1 -nomaskinterp -stop SD_PROB FODsh.mif fibers.tck

But then some of the selected fibers end inside the WM... Assigning them to the nearest GM region doesn't seem realistic.

I tried to run using '-include ROI1.nii -include ROI2.nii' where ROI1 and ROI2 are both copies of the GM_dil_mask, but it didn't change the output. Running the command without the "-mask" option didn't help either.

I thought about running streamtrack separately for each of the GM dilated regions, using ROI1 = the corresponding dilated GM region and ROI2 = all other dilated regions, and then concatenate all the track files, but this would bias the tracking because of the different sizes of the GM regions right ?

Does anyone have an idea on how I could proceed ?

Thanks in advance and best regards,
David Romascano
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