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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 > ---------------------------------- >