 |
 |
Hi, what do you mean by grey voxels? Do you use the functional data as thresholded z-map, or do you try to run the call on a rendered image that overlaid the statistics on the structural brain. For the latter I won't be surprised, if it also uses the grey voxels of your structural image. Use this call on the thresholdes z-stat image, and it should work. fslstats your_roi -V # should give the number of voxels / volume of your roi fslstats your_funcdata -k your_roi -V # gives the number of voxels within this roi, that are superthreshold (as long you use the stats image only) good luck, wolf On 31/08/11 16:57, Mathias Warnke wrote: > Thanks Wolf > > I tried this option but i think there must be some extra way to > threshold the func data first because it seems that the -V option also > considers the gray scale voxels. > > your help will be greatly appreciated. > > Best regards. > > 2011/8/30 wolf zinke <[log in to unmask] > <mailto:[log in to unmask]>> > > On 30/08/11 22:19, Mathias Warnke wrote: > > Hi FSL forum. > > Can anyone help me determining the amount of activated voxels > contained within a userdefined ROI? > I have used some commands like --volume and fslmaths but I'm > afraid it returns the whole voxels inside > a ROI and not only the activated voxels I want to assess (see > the attached image). I.e. these commands > output the anatomical scan plus the activated voxels. > > Thanks in advanced. > > Best regards. > > Hi > > Try: fslstats your_funcdata -k your_roi -V > > I think that's doing what you want. > > good luck, > wolf > >