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Hi again. Sorry for the disturbance. A binary mask was mandatory for the versions FSL 4.0.* and below. With versions higher than that Probtrackx should work fine also with non-binary masks. However when importing SPM data into FSL you will have to FLIRT the data, as the origins and the dimensions are not the same ( -1 comming form SPM due to the Matlab / C++ counting problem). This gives you transformations that will change your values (due to reslicing) and it is easier to control for that if the mask is binary. best, Markus 2009/11/23 Alessio Moscato <[log in to unmask]>: > Hi all.. reading this last makes me worry about the masking process.. my > question is: is it necessary to use binary masks for > seeding/waypointing/excluding/terminating? I often use fMRI FEAT activations > for seeding or waypointing.. but these activations never are only binary.. > Since now I haven't noticed any problem.. but, at this point, I have the > doubt that some problem exists and I don't see it... > Any suggestion? > All the Best > Dr. Alessio Moscato > Medical Physicist > Medical Physics Dep., Niguarda Hospital > Milan, Italy > > On Mon, Nov 23, 2009 at 10:08 AM, Markus Gschwind <[log in to unmask]> > wrote: >> >> Hi! >> >> Sure, you can. >> Make sure that the mask is binary and that it is in the good >> dimensions by fslview + add overlay. >> >> If it is a cortical blob you want to take the mask from then it might >> be necessary to grow it into the white matter first. >> >> Best, >> Markus >> >> >> >> 2009/11/23 shantanu ghosh <[log in to unmask]>: >> > Dear FSL users, >> > >> > can i use SPM.mat generated by SPM2/8 as a mask for constraining fibre >> > tracking in FSL? Any help is appreciated. Thanks in advance. >> > >> > shantanu >> > >> > ________________________________ >> > The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. >> >> >> >> -- >> >> >> Dr. med. Markus Gschwind, M.D. >> Laboratory for Neurology and Imaging of Cognition - Dept of Neurosciences >> University Medical Center (CMU) >> 1, Michel-Servet >> CH-1211 GENEVA - Switzerland >> >> Tel 0041 (0) 22 379 5324 >> Fax 0041 (0) 22 379 5402 >> email: [log in to unmask] >> http://labnic.unige.ch > > -- Dr. med. Markus Gschwind, M.D. Laboratory for Neurology and Imaging of Cognition - Dept of Neurosciences University Medical Center (CMU) 1, Michel-Servet CH-1211 GENEVA - Switzerland Tel 0041 (0) 22 379 5324 Fax 0041 (0) 22 379 5402 email: [log in to unmask] http://labnic.unige.ch