# Fiber(column) tracking in the gray matter **URL:** \ **Category:** Uncategorized\ **Created:** [March 17, 2019, 2:55pm UTC](https://community.mrtrix.org/t/fiber-column-tracking-in-the-gray-matter/2368 "2019-03-17T14:55:45Z")\ **Posts on this page:** 1\ **Showing post:** 4
**Author:** ![ThijsDhollander](https://community.mrtrix.org/user_avatar/community.mrtrix.org/thijsdhollander/32/1617_2.png) [@ThijsDhollander](https://community.mrtrix.org/u/ThijsDhollander)\ **Post date:** [April 7, 2019, 3:35am UTC](https://community.mrtrix.org/t/fiber-column-tracking-in-the-gray-matter/2368/4 "2019-04-07T03:35:20Z")
Hi @Yixin_Ma, In this context, you might be particularly interested in the upcoming MACT (Mesh-based ACT) framework developed by @chunhungyeh from our group / the MRtrix3 team: it’ll allow for _some_ of the discussed alterations to be performed more directly, in a less hacky or even properly hack-free way. See his post below for some details on the topic: > [@MRtrix tutorial available on OSF](https://community.mrtrix.org/t/mrtrix-tutorial-available-on-osf/1942/32): > > Hi @schilkg1, > > While it might be inappropriate to have a lengthy discussion within this post, I do wish to clarify some points respecting your 2nd and 3rd questions. Please see below. > > ![](https://community.mrtrix.org/letter_avatar_proxy/v2/letter/s/c67d28/40.png) schilkg1: > > > What happens if the streamlines stop just short of labels (for example if my labels don’t exactly align or match the WM/GM boundary)? Will they not be counted in the connectome generation? > > Good question. We did have spotted on the _misalignment_ issue that you mentioned here; indeed, only ~25% of streamlines will be used in the connectome largely because of such misalignment. We describe it as a _source data mismatch_ problem: the WM/GM boundary derived from tissue partial volume maps (based on tissue segmentation) used in tractography is not always consistent with the boundary of brain parcellation images used in connectome construction. Performing a 2-mm search from streamline endpoints (to find the nearest labelled voxel ) is the current _MRtrix3_ ’s default mechanism implemented in `tck2connectome` to deal with such inconsistencies (see the `-assignment_radial_search` in the help page of `tck2connectome` ). Using the radial search, ~85% of streamlines will contribute to the outcome connectome. If interested, please see [this abstract](https://www.researchgate.net/publication/307862648_The_influence_of_node_assignment_strategies_and_track_termination_criteria_on_diffusion_MRI-based_structural_connectomics) for the relevant influences. > > ![](https://community.mrtrix.org/letter_avatar_proxy/v2/letter/s/c67d28/40.png) schilkg1: > > > Does MRTrix have any capabilities for connectome generations using meshes as opposed to labels? For example mesh of WM/GM interface or mid-cortex mesh. Similarly, can meshes be used, for use with anatomical constrained tractography, or should this be converted to binary masks? > > To avoid losing precision, my approach to deal with the _source data mismatch_ is directly using high-resolution tissue surface meshes to _unify_ the source data: the same labelled surfaces are used for both tractography and connectome generation, as described in your question. I called this method _Mesh-based ACT_ (or _MACT_ ), where streamline endpoints are the intersection points between streamlines and the labelled surfaces (cortical and sub-cortical WM/GM surfaces). When using MACT for connectome generation, there is no need to convert, for example, the vertex-wise labels of HCP-MMP into volume-based labelled images. > > For more details, please see [MACT abstract](https://www.researchgate.net/publication/315836374_Mesh-based_anatomically-constrained_tractography_for_effective_tracking_termination_and_structural_connectome_construction) for reference. If you registered the ISMRM2017 meeting, I think my presentation video ([0058](https://www.ismrm.org/17/program_files/O71.htm)) should still be accessible, there are more explanations on the background and the principle of MACT. > > Finally, about using a mid-cortex mesh, I believe that it would only require a simple change in MACT. Coincidentally, I did once consider using a mid-cortex mesh as a default setting (rather than taking both inner and outer cortical GM surfaces). If you or anyone see any potential benefits or applications of using mid-cortex, I’d love to hear your insights and recommendations. So, even though MACT is not yet available in _MRtrix3_ , it has already and still received serious development by me and has been applied to a few studies. Any queries about MACT are very much welcome; please let me know via a personal message or an email. > > Many thanks. The original post (in its original context) can be found here: [MRtrix tutorial available on OSF - #32 by chunhungyeh](http://community.mrtrix.org/t/mrtrix-tutorial-available-on-osf/1942/32) . Cheers, Thijs --- _[View the full topic](https://community.mrtrix.org/t/fiber-column-tracking-in-the-gray-matter/2368)._