tck2connectome for mean streamline lengths

1

Hi everyone,

I am using MRtrix tck2connectome command to extract streamline lengths. I first convert freesurfer destrieux parcellation (aparc.a2009s+aseg.mgz) to a mif file to use in MRtrix by using following command:

labelconvert /mnt/c/users/muhammed/desktop/capa_yedek/CAPA-00026/Processed/CAPA-00026.par.nii $FREESURFER_HOME/FreeSurferColorLUT.txt /home/mu_linux/mrtrix3/share/mrtrix3/labelconvert/fs_a2009s.txt capa_dest.mif

I obtained tck file by using DSI studio.

When I run tck2connectome command:
tck2connectome /mnt/c/Users/Muhammed/Desktop/capa_new/wb1.tck capa_dest.mif distances1.csv -scale_length -stat_edge mean

I get following error:
[WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164
tck2connectome: [WARNING] (This may indicate a poor registration)

What could be reason for this. I could not find any information. Thanks for your help.

3

I recognize that the coordinates of the tck file obtained from DSI studio is different from the parcellation file. I tried to solve the problem but could not find any solution. How can I transform the track file to dwi native space.

4

Welcome Muhammed!

You will need to take a close look at whatever mechanism was used to convert from DSI Studio’s own tractography file format into the .tck file format. It’s not a matter of “transforming to dwi native space” so much as the reference axes that are assumed as part of the format. As is the case throughout MRtrix3, we use the hardware scanner axes as the reference; so-called “real space” or “scanner space”. Many other softwares define streamline vertices (among other information) based on the voxel grid of some reference image. If proper conversion between these two is not performed, then the streamlines will experience an unwanted transformation. This is the most likely explanation for the effect you’re seeing; but how to fix it will depend on what you’re currently using for that purpose (and indeed whether anyone can suggest an alternative; I don’t interact with other DWI analysis softwares a great deal so am not the best source).

Cheers
Rob