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Hi > Hello, thanks for the response. You mean with probtrackx2 I don't have to enter the --mesh parameter? Yes that's right. > > I want to use as seed a ROI in the left heliosphere and as classification targets one ROI of the left and one of the right. As I understand to include the targets I write their paths in a file and give it as --targetmasks parameter. Do I need to include that file with my targets also in the parameter --waypoints?? or I don't need to pass it twice? Use waypoint if you want to use an inclusion mask. the --targetmasks option will only do the counting, it will not exclude streamlines that do not pass through the targets. > Oh, I thought I could enter for the paremeter -x a .label file. So it needs to be a .mgh file? You can't use the label file, as these do not contain surface information. You can't use .mgh either. Please have a look at the doc to see which file formats are available. Cheers Saad > > Thank you, > > Le lundi 8 octobre 2012, Saad Jbabdi a écrit : > Hi > > I would recommend using probtrackx2 for this, as unlike probtrackx, you don't need a surface description: probtrackx2 does not assume that you are using just one surface, but instead each ROI mask defines its own surface. > > If you need both hemispheres (e.g. one where the seed is and one where the waypoint mask is) then you should use both surfaces. > > I am assuming your seed/target masks are freesurfer label files? In this case, you will need to transform these into surface files using label2surf (seed the doc) > > Cheers > Saad > > > On 8 Oct 2012, at 05:38, Monica Giraldo wrote: > > > Dear FSL experts, I'm trying to run tracktography between a region in left hemisphere to a region in the right one using freesurfer surfaces. I don't know what file to put as a description of the whole cortical surface. In FSL page you recommend lh.white.asc if Left hemisphere and rh...etc if right hemisphere .... But if I'm tracking in both hemispheres then what file I put? I see in the folder mri (from the output of freesurfer) a wm.mgz file but is not a label file. > > Sorry, I'm new with freesurfer. I was thinking on passing that .mgz to nifti as you tell to do with the brain.mgz in tutorial and use that but I'm not sure. > > > > Thanks, > > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.fmrib.ox.ac.uk/~saad > > > -- > Mónica Giraldo Chica > PhD student in Biomedicine > University of Barcelona (Spain) - York University (Canada) > Neuroimaging Laboratory > 1008 Sherman Health Science Research Center. Toronto, Canada > www.monicagiraldochica.com > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad