How to reconstruct tracts within a specific cortical region?

1

Hi everyone,

I want to reconstruct tracts within a specific cortical region, ie. the seed region and endpoint region are both the specific cortical region.

I have tried tckgen wmfod.mif tracks_1.tck -act 5tt_coreg.mif -backtrack -select 100000 -seed_image mask -include_ordered mask -seed_unidirectional
and double “-include_ordered”:
tckgen wmfod.mif tracks_1.tck -act 5tt_coreg.mif -backtrack -select 100000 -seed_image mask -include_ordered mask include_ordered mask -seed_unidirectional
But none of the above get the good result :joy:

So what should I do?

Thanks in advance for any advice,

Panshi

2

Supplementary diagram: I want to reconstruct the brown tracts
_20220523165705

3

Hi Panshi

What qualifies as a good / bad result?

I think having identical masks for seeding and including is not going to get you anywhere, since any streamline will have already fulfilled your inclusion criteria simply by existing…
I would suggest using two ROIs (you can make them very thin so in anatomical terms they’re practically identical), with the include one “behind” the seed one, and using the -stop flag. Maybe also use -maxlength to get only “local” streamlines.

e.g. I used the following command:

tckgen fod.mif -seed_image yellow_roi.mif -include pink_roi.mif -seed_unidirectional -select 100 -stop -maxlength 50 test_out.tck

to get this (crosssection view; ROIs are single slice disks):

Test
Test706×782 138 KB