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Hi! Thank you for your helping and your explanation. I will try it Best regards, Rosalia. 2013/4/3 SG KIM <[log in to unmask]> > Hi Rosalia, > > I actually haven't tried the function "atlasquery" before, but now I find > it quite handy. > > Here's an example: > > $ atlasquery -a "Harvard-Oxford Subcortical Structural Atlas" -m > MNI152_T1_2mm-mask.nii.gz > Left Cerebral White Matter:20.5 > Left Cerebral Cortex :44 > > The mask file here includes only two voxels: (GM 39%; WM 22%) and (GM 49%, > WM 19%) in HO-sub atlas, so it shows the averages of probability labels for > a given mask. > > Now you need to make a binary mask with suprathreshold (say, alpha=0.05) > voxels: > > $ fslmaths <1-pval_result> -uthr 0.95 -bin <mask> > > and put this <mask> file into atlasquery: > > $ atlasquery -a "JHU White-Matter Tractography Atlas" -m <mask> > > and you get a list of averaged probabilities. > > Best, > --- > Seung-Goo KIM > > On 3, Apr, 2013, at 10:50 AM, Rosalia Dacosta Aguayo wrote: > > Hi Seung-Goo > > Many thanks for your kind and helping explantion. If you do not mind, I am > going to send you two images to your personal mail because FSL mailing list > do will not support them....with the coordinates...in order to guess how > can I get more information about the cluster. > > Best regards, > Rosalia. > > 2013/4/2 SG KIM <[log in to unmask]> > >> Hi Rosalia, >> >> I guess you actually told us the voxel indices of (55,125,38), which >> corresponds to (35.0, -2.0, -34.0) MNI-coordinate and according to other >> atlas tool values: white matter voxel in the anterior part of right >> temporal lobe. >> >> If it is correct, first you should know that neither ICBM-DTI-81 nor JHU >> WM atlas cover whole white matter voxels, because the atlases only specify >> some of well-known major fiber bundles; thus many of white matter voxels in >> fine tracts are not classified for many issues. >> >> And second, you may want to look at the values from other voxels of the >> cluster you found, not only the one peak voxel. You may have more >> information about the cluster (say, whether it is likely to be part of >> uncinate fasciculus or inferior longitudinal fasiculus). >> >> >> Best, >> --- >> Seung-Goo KIM >> >> On 2, Apr, 2013, at 10:13 PM, Rosalia Dacosta Aguayo wrote: >> >> >> Dear FSL experts, sorry for posting this mail again. >> >> I am having some problems with the anatomical identification of some of >> my tbss results. >> >> For example: one of my results give me the following MNI coordinates: >> 55-124-38 of a cluster size of 1758 mm(3). >> >> When I open Fslview, load the image and write the coordinates, the >> message I get is "label not found": >> >> Harvard-Oxford Subcortical Structural Atlas >> 69% Right Cerebral White Matter, 30% Right Cerebral Cortex >> JHU ICBM-DTI-81 White-Matter Labels >> Unclassified >> JHU White-Matter Tractography Atlas >> No label found >> >> Any one could help me with this? >> >> Yours sincerely, >> Rosalia. >> >> >> > >