# 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:** 6
**Author:** ![chunhungyeh](https://community.mrtrix.org/user_avatar/community.mrtrix.org/chunhungyeh/32/4570_2.png) [@chunhungyeh](https://community.mrtrix.org/u/chunhungyeh)\ **Post date:** [April 8, 2019, 10:42am UTC](https://community.mrtrix.org/t/fiber-column-tracking-in-the-gray-matter/2368/6 "2019-04-08T10:42:56Z")
Hi @Yixin_Ma, > [@Yixin\_Ma](#): > > The anatomical-contrast image that I have is 1x1x1 mm3 isotropic whole brain volume. This resolution value was chosen because FreeSurfer reconstruction works best with 1mm isotropic voxel size. I can use the image prior generated from Freesurfer to hack the 5TT image, as you described. > [@rsmith](#): > > Now that’s not to say that ACT _can’t_ track through the cortex, in fact it only requires a very simple tweak: Take the “cortical GM” volume from the 5TT image, add those partial volume fractions to the “Sub-cortical GM” volume, and then null the “Cortical GM” volume (they’re really more like “GM-you-can’t-track-through” and “GM-you-can-track-through” images…). That’s not to say this is a solution specifically for what you’ve asked here, I just wanted to explain that in case it’s relevant for yourself or anyone else interested in cortical columns. > [@rsmith](#): > > So for instance: You could re-map the cortical segmentation to volume 2 (“WM”), and re-map both the CSF and WM segmentations to volume 0 (“Cortical GM”). Then, streamlines would only be permitted to exist within the cortical ribbon, and a streamline would need to reach either CSF or WM at both endpoints in order to be deemed satisfactory according to your imposed priors. I’ll throw in my two cents: If you are going to take the methods above, there are a few things to watch out: The groove of a sulcus can be very tiny and sometimes not really visible/detectable on T1 due to limited image resolution (i.e. the partial volume effect). So, there are good chances that streamlines may transverse across the gap of the sulcus. Similar effects may occur in other brain areas, a few examples here: cross-hemisphere streamlines could appear in regions where the cortices of both hemispheres attached to each other on the images; likewise, there are also good chances that streamlines would directly enter cerebellum from temporal or occipital lobe. So for tracking in cortical columns, unless having very high-resolution T1-weighted images or a decent tissue segmentation algorithm, I personally think that the methods suggested above probably require more fine adjustments either in `5ttgen` or in ACT. > [@Yixin\_Ma](#): > > I do have some detailing questions regarding this, what if the anatomical image needs to be registered to the DTI volume (e.g., DTI is a slab of oblique coronal slices with the resolution of 0.625x0.625x2.6 mm3, and the anatomical image is whole-brain with the resolution of1x1x1 mm3). The mesh of the cortical surface will be generated based on the anatomical image (1x1x1mm3) using FreeSurfer. In that case, will the mesh file handle the mismatch of voxel size and a 6 dof rotation? If not, how should I pre-process the images before putting them into the MACT model? If I understand correctly, your concern is about the alignment of the surface meshes with the DWI data, is that right? I usually use SPM to register T1 to DWI for intra-subject registration (motion correction), which only modifies the transformation info stored in T1’s header, i.e. T1s are not resampled to voxel dimension of DWI data. Then, I run surface reconstruction on the registered T1s (of the original resolution), so there is no need to apply a rigid-body transform to the meshes. For your reference, MACT already uses both outer and inner cortical grey matter surfaces (e.g. FreeSurfer’s pial and white surfaces) as anatomical references, and has the mechanism to avoid issues like cross-sulcus tracking and so forth. I think it would be simple to customise MACT codes for your need, if tracking in the cortical column is what you are aiming for. Cheers. Jimmy --- _[View the full topic](https://community.mrtrix.org/t/fiber-column-tracking-in-the-gray-matter/2368)._