Hi András,

I would check if lrmask has some nonzero voxels:

fslstats lrmask.nii.gz -V

Are the seeds in the same space than DTI space ?

Moises.

On 14 October 2015 at 21:25, Dr. András Jakab <[log in to unmask]> wrote:

Dear FSL list

I am running probtrackx / probtrackx2 to output a  seed2lowresmask connectivity matrix for connectivity-based segmentation in matlab. While this was successful for many cases, using data from somewhere else results in an empty matrix. I would be open for your suggestions on what could go wrong and what further debug steps should I make.

- seed and lrmask is in the same space, same orientation and data order, etc (with fslhd)

- fdt_paths.nii.gz seems OK, nice summed tracts appear, so the tractography itself runs correctly

- fdt_matrix2 has dimensions of 5167*1*1*1 instead of seed*lowres 

- with probtracxk2, the fdt_matrix2.dot has only 1 entries, 5167 0 0 

- the program was not terminated prematurely, it runs for a proper amount of time

syntax so far:

probtrackx2 -x thalamus-left.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd --pd -s bedpostx.bedpostX/merged -m bedpostx.bedpostX/nodif_brain_mask --dir=left-thalamus --target2=lrmask.nii.gz --omatrix2 fdt_matrix2

Thanks a lot,

András

--

Dr. med. Andras Jakab, PhD

Marie Curie Post Doctoral Researcher
Computational Image Analysis and Radiology Lab
Medizinische Universität Wien
Universitätsklinik für Radiologie und Nuklearmedizin
Währinger Gürtel 18-20
A-1090 Wien

Cellular: +36305095083

----------------------------------