Whole brain Tractography tracts coordinates

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Oct 22, 2018, 8:13:08 AM10/22/18
to ExploreDTI

I've been doing whole brain tractography, and using the resulting tracts file for other analysis.
when trying to use the coordinates in the native DWI space, the coordinates don't fit the image size (not as voxels and not as mm). What type of coordinates are those, and can they be converted back to native space voxel/mm coordinates?

Julián Marino

Oct 22, 2018, 8:49:59 AM10/22/18
to ron...@mail.tau.ac.il, E_...@googlegroups.com
Dear Ronniek,

When you talk about native space, I assume considering differences between the initial native space and the post-processing steps. ExploreDTI doesn't use a standard coordinate system like MNI or Talairach, as you know. Explore DTI coordinates are sensitive to acquisition FOV, then, be cautious with the black space surrounding parenchyma, because it is included in the ExploreDTI coordinate system. I suggest you register T1 of the whole brain in a template (MNI). But, I comprehend you as maintaining native space without parametrical using templates. Then, take your voxel array, for instance: [2 2 2], and go front to back, left to right and top to down. Ignore surrounding space. Translate it to cubic millimetres. ¿The volume is metrically ordinary? Meanwhile, download Tailarach Daemon and MNI to Talairach and vice versa conversion. If helping you, in our institute, native space measures of each 3D are considered [ 1 1 1 ]. If you like to differentiate about native spaces distances, it functions. Applying a simple mathematical rule, the cingulum genu of each native space position can be compared intersubject. 

Best for you, remember that the first step is to assure that acquisition throw you right metric measures considering complete FOV.

Julián, CCLINEC, Puerto Madryn, Patagonia


 Julián Marino Dávolos; PhD.

Tractographical Neuropsychology
Universidad del Chubut- CCLINEC- Patagonia 

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Oct 22, 2018, 9:07:13 AM10/22/18
to ExploreDTI
I'm trying to load the .mat file and use the coordinates as coordinates for the data object from the .nii or .mat DWI file.
are you saying the coordinates are based on the brain area, not including the blank spaces around it? it still doesnt fit in size (I've a (92,92,58) image [2 2 2] and the coordinates I get go up to 190 on every axis).
is there a

Julián Marino

Oct 22, 2018, 9:44:21 AM10/22/18
to ron...@mail.tau.ac.il, E_...@googlegroups.com
Dear Ronniek, Explore DTI, as you can prove, use all the FOV. Black space (or 0 value in.mat) are taking account in ExploreDTI, but if you want to use ExploreDTI informing coordinates, you need to delete the useless [ 0 ] space. ExploreDTI philosophy isn't a parametric spatial statistics factory. Then, manually calculate parenchyma native space size using boundaries cairns (occipital pole, frontal pole....). 
Applying a simple mathematical rule to perform what you want, use [ 1 1 1] for [ X Y Z ],  then, you will be using coordinates to inform and make comparisons. Of course, Talso to make comparisons have ATBS, or/and b) do the mathematical handcraft [ 1 1 1 ] method. 

Recapitulation: Black- zero FOV space are considered in ExploreDTI 'coordinates', but you are not interested in black- zero part. 
At first, remember to be sure what you have in your hands. Taking into account your voxel size, in millimetres, ¿how long, wide and high are the native space you have? Don't include black-0 space. Translate it into [ Xmm Ymm Zmm ]

Best, Julián 

Juan Arias

Oct 23, 2018, 10:18:04 AM10/23/18
to ExploreDTI
Hi Ronniek,

your problem seems to be that the 3D coordinates of the tractography file (when you inspect it in MATLAB) are much greater than the 3D coordinates of the diffusion image (in voxels as well as in mm). As Julián said, you should be careful with processing steps applied after generating the tracts, as they might compromise spatial correspondence (e.g. FOV cropping).

When you load the tractography file in MATLAB, you will see numerous variables, most of which contain information split first by tract and then by points (which were defined during the pathway propagation process). Points have spatial locations within voxels, so the 3D coordinates for each point of a pathway (see the variable 'Tracts' for 3D coordinates of each point of each pathway) are defined in mm. Given that ExploreDTI uses radiological convention, 3D coordinates should increase from right to left, down to top, and front to back.

If you see values greater than [(voxel size in dimension X-Y-Z) * (number of voxels along dimension X-Y-Z)] you might want to directly check if there is spatial correspondence between the tractography file and the diffusion image by: (a) seeing if the variable 'TractMask' is equal in dimensions to those of your diffusion image, as well as (b) seeing if the variable 'VDims' is equal in dimensions to those of the voxels in your image. If it isn't, could you rerun whole-brain tractography with default settings for one case and check if the problem persists?

Should you need further assistance, feel free to write again.



CCLINEC - Argentina
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