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The output of single voxel tractography to the whole brain (define single seed, no classification mask, ventricular exclusion, usual default parameters); repeat x MANY I end off with id_region_1_1_1.nii.gz id_region_1_1_2.nii.gz id_region_1_1_3.nii.gz : etc, etc., Is there a way to get each single output as an individual array? (i.e. Value,Location for all voxels >0)) Thanks, - Chris Saad Jbabdi wrote: > Hi Chris, > > Which probtrackx output are you talking about? Is it the fdt_paths files or the target-based classification results? (i.e. seed_to_<target>.nii.gz) > > In the latter case, you can use the --s2tastext option, which will produce a ascii text file summarising the seed-to-target classification results. > > > Cheers, > Saad. > > > > > On 2 Jun 2010, at 11:17, Christian Lambert wrote: > > >> Morning, >> >> I'm looking to change somehow my output of probtrackx. I have a bottleneck in processing which is the reading of .nii.gz files (unzip->read data->del unzipped). I have refined every other aspect of my scripts but get stuck at this point, resulting in processing times of 3-4 days + (17000-30000 files) purely from file reading (in matlab). I convert and handle all my dti data in array format for memory and speed (so purely value and location in seed source space (where value is >0) enabling simple reconstruction where required). >> >> Is there anyway to roll this into the probtrackx pipeline, maybe outputting the info as a .txt or similar? >> >> Thanks, >> >> - Chris >> >> > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.fmrib.ox.ac.uk/~saad > > >