Small issue with tckgen

1

Hello,

I’m having a small issue and hope you all could take a minute to help out! tckgen is giving me this error:

$ tckgen cebdm35014_FOD.nii.gz 35014.tck -number 10M
tckgen: [ERROR] Must provide at least one source of streamline seeds!

It was my understanding that the FOD acquired through dwi2fod would be my source for tckgen, but it seems this is not the case. Below is the code I used for dwi2fod:

dwi2fod csd ${OUTPUT}/cebdm${SUBJ2}.nii.gz ${OUTPUT}/cebdm${SUBJ2}_out.txt ${OUTPUT}/cebdm${SUBJ2}_FOD.nii.gz -mask ${OUTPUT}/cebdm${SUBJ2}_mask.nii.gz -fslgrad ${OUTPUT}/e${SUBJ2}_bvecs ${OUTPUT}/e${SUBJ2}_bvals

What am I missing? Thank you in advance :slight_smile:

2

Hi @aszymanski,

tckgen uses a fairly clear distinction between the mechanism used to determine seed points to initialise streamlines propagation, and the image data used by the streamlines algorithm to determine the direction in which to subsequently propagate the streamlines.

In the tckgen help page, there’s a section “Tractography seeding options”, which describes all of the different mechanisms that can be used to determine where the streamline seed points should be drawn. This flexibility allows a very wide range of tracking experiment designs. You need to provide at least one of these options, otherwise tckgen doesn’t know where to put the seed points.

Cheers
Rob

3

I see, thank you!