Visualize a tractogram

1

Hi,

I have a .trk file. I am unable to download trackvis in my computer. May I know what is another way to visualize a tractogram file? The reason I want to visualize is to know if the b-vector files used to generate the tractogram are fine or if they have been flipped. Or can we know if the b-vector files are fine from our structural connectivity matrix?

Thanks and regards,
Jagruti Patel

2

Hi Jagruti,

DIPY and FURY have several ways to visualize trk files. For details, you can see this example that we created for the pyAFQ project: Visualizing AFQ derivatives — AFQ 1.1 documentation.

Alternatively, if you want a GUI to work with MIBRAIN is a great choice: Release 2020.04.09 · imeka/mi-brain · GitHub

Cheers,
Ariel

3

Hi @Ariel_Rokem ,

Thanks a lot for the reply. May I know how to know if the b-vector tables are fine or they have been flipped? Can we know this by looking at the images itself or the structural connectome? Or this can only be solved by looking at the tractograms?

Thanks and regards,
Jagruti Patel

4

Hi @jagruti8,

You can use dwigradcheck from MRtrix3.

Best,
Steven

5

Hi @Steven,

Thanks a lot for the reply.

With best regards,
Jagruti Patel

6

FSLeyes also has some support for visualising TrackVis and MRtrix3 tractograms - more details can be found at Overlays — FSLeyes documentation