Hi experts,

I have been running tracking between a couple of regions, and now I'd like to build a group mask. For doing this I first have to apply a probabilistic threshold to the individual fdt_paths.nii.gz.

I have run the tractography with nonlinear transformation to the standard MNI 2mm space, and I have used waypoint regions in this standard space using the network option as follows:

probtrackx2 --network -x MASKS -l --onewaycondition --avoid=cerebell  -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=MNI_to_dif_nolin.nii.gz --invxfm=dif_to_MNI_nolin.nii.gz --forcedir --opd -s bedpost.bedpostX/merged -m bedpost.bedpostX/nodif_brain_mask --dir=RESULT

The question is: although the resulting fdt_paths is in this standard space, the tractography has been run in the diffusion space and after that tranformed to the standard? or has it been run directly in the standard space?

I need to know this to divide the maps by the number of seeds*voxels in order to transform the counting maps to probabilities.

Thanks!

Jose

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José Angel Pineda Pardo

Center of Biomedical Technology (CTB)

Parque Científico y Tecnológico de la UPM

Campus de Montegancedo

28223 Pozuelo de Alarcón, Madrid, ES