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Hi - The command-line usage is indeed a bit unclear, apologies! In probtrackx, the --mode is only used in the context of a single voxel tractography, in which case you use --mode=simple. There are three other ways of running probtrackx, and no call for -- mode is required: 1. seed mask, using -x <seed> 2. two masks: using -x <seed> together with --mask2=<secondmask> 3. network: using -x <textfile> --network The two masks mode is exactly equivalent to the network mode with where the input <textfile> that has two entries. In both cases, tractography in ran from the first seed and the second as waypoint, then the other way round. As for your second question: > The other thing was that I also would like the information about > the number > of included paths that you get from the waypoints.txt file. This > does not > appear to be generated with the current command line setup I am > using. Do I > need to set some extra option to produce this? Or is that > information not > available when specifying two seeds in an ascii file like this? I don't really understand what you mean by : "the number of included paths that you get from the waypoints.txt file". Do you mean "waytotal"?? In this case, the waytotal file is only available when using option 1 (i.e. single seed mask). Cheers, Saad. On 2 Jul 2008, at 18:07, John D. Griffiths wrote: > Hello. > > I have some questions about fdt command line usage, if you > don't mind. > > I want to do two-mask symmetric tracking, but I understand > that this > option is no longer available as a field in the command line input. > I have > tried doing this with the '--seed' and '--mask2' options, as suggested > elsewhere on the mailing list, but simply cannot find the right > combination > of commands to get this to work. Could you please give an example > of the > correct command line input to use these options properly? > > So I have instead been creating ASCII files, each with 2 lines > specifying > the locations of the two seed images I want to use. This only seems > to work > when the command contains the terms '--network --mode=seedmask'. > I'm not > sure whether this is doing what I want though: I want to include > only fibres > passing through both masks. Do I need a different command for this? > > The other thing was that I also would like the information about > the number > of included paths that you get from the waypoints.txt file. This > does not > appear to be generated with the current command line setup I am > using. Do I > need to set some extra option to produce this? Or is that > information not > available when specifying two seeds in an ascii file like this? > > > [Here is an example of the command I am using: > > probtrackx --network --mode=seedmask -x > /work/imaging4/Structural/CBU_DTI/pCBU080311/Tractography/ > Native_Space_Seeds/Wakana_et_al_ROIs/SLF/Left_Temporal_SLF/ > Left_Temporal_SLF_masks.txt > -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s > /work/imaging4/Structural/CBU_DTI/pCBU080311/fsl_analysis.bedpostX/ > merged -m > /work/imaging4/Structural/CBU_DTI/pCBU080311/fsl_analysis.bedpostX/ > nodif_brain_mask > --dir=/work/imaging4/Structural/CBU_DTI/pCBU080311/Tractography/ > Native_Space_Seeds/Wakana_et_al_ROIs/SLF/Left_Temporal_SLF > > > > Thanks, > John Griffiths > (CSLB. U.o.Cambridge) > ------------------------------------------------------------------------ --- Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222545 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~saad ------------------------------------------------------------------------ ---