Hi Francesco,

The omatrix1 option gives you the connectivity matrix between your seed voxels. So if you set your mask of the thalamus as the seed mask, you would get a connectivity between the thalamic voxels (NxN matrix), not between the thalamic voxels and the cortical regions (Nx6 matrix). If you want the latter you should run probtrackx with the —os2t option and the —targetmasks=<filename>, where the filename is a text file containing the filenames of the 6 cortical masks (see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Classification_targets for how to do this in the GUI).

Afterwards you could use the `find_the_biggest` command to segment the thalamus based on which cortical mask it is most likely to be connected to (see http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt2/index.html#conseg).

Best wishes,

Michiel

On 2 Feb 2018, at 03:05, Francesco Sammartino <[log in to unmask]> wrote:

Hi everyone

I am trying to parcellate the thalamus using 6 cortical masks and omatrix1 option.How can I order the fdt_matrix1.dot file afterwards?

I guess I can still use kmeans as in matrix2 but without running cross correlation this time?

Thanks a lot

Francesco Sammartino 

On Jan 30, 2018 4:03 AM, "Dave Yas" <[log in to unmask]> wrote:

Hi,

I am getting a blank FA file after running DTIFIT on all my subjects.

I ran BET, then Eddy current, then DTIFIT.

The previous steps were okay, but I had a problem with this step (DTIFIT).

I got no error messages everything ran smoothly which is why i don't know what hints to give.

Can someone help please?

Dave