Tck scalar file


#1

Hi experts

I was wondering how to obtain a scalar file of a track already generated based on the probabilisitic information of the track itself?

Thank you!


#2

Hi @josue_avecillas

By scalar file do you mean something like this?

If so, the command you are looking for is tckmap


#3

Hi @cbajada, thank you for your answer. I am looking for a scalar file that can be used to threshold the streamlines based on the probabilistic information of the TDI image that you are showing. The scalar file is used in the “color” section of the tractography tab on mrview.

Thank you so much!


#4

Hi @josue_avecillas,

Colouring / thresholding streamlines within the mrview Tractography tool based on an external file can be done in one of two ways:

  • A text file that contains one value for every streamline; each streamline will then be coloured uniformly along its length according to the corresponding value / shown or not shown depending on the corresponding value.

  • A Track Scalar File (TSF); unfortunately this format is still not yet described in the documentation, but in brief it provides a value per streamline vertex, that can therefore be used to colour / hide individual streamline vertices; so streamlines can change in colour along their length, and sub-sections of each streamline can be shown / hidden.

The most accessible way of generating such files is the tcksample command. However from your descriptions:

… obtain a scalar file of a track already generated based on the probabilisitic information of the track itself

… based on the probabilistic information of the TDI image …

, it’s unclear exactly what type of information you are trying to encode / extract.

Rob


#5

Hi @rsmith

I obtained my threshold file using tcksample!

Thank you so much