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On 4 April 2017 at 12:33, Robert Mok <[log in to unmask]> wrote: > I just wanted to check if there is an easier way to find the cluster of > interest? I have been trying to find some clusters and sometimes it's hard > (e.g. because it joins with another larger cluster). Or some semi-automised > way to find the clusters? > Well, if it joins another cluster it's technically one cluster! > > e.g. in an ideal world, i can find approx location of the peak of the > cluster i want, then algorithm tells me what threshold to use. or more > likely possible, adjust the threshold, then select the cluster in order to > 'find' it (rather than try to find it again on the cluster table..). > > I think people sometimes write ad-hoc things for this sort of thing, but I think there's always going to be cases when it's unclear which is the right approach, and it could be hard to justify. I guess a simple solution if you want one is to take your peak voxels, and include voxels within a certain radius that are also in the same cluster (look at *https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;de8e9a62.0802 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;de8e9a62.0802> *for a how to create a spherical mask ). Eugene > Thanks! > Rob > > ------------------------------ > *From:* Robert Mok > *Sent:* 01 April 2017 22:52 > *To:* FSL - FMRIB's Software Library > *Subject:* RE: [FSL] Creating mask from localiser scan - selecting a > cluster / exclude others > > Ah - I should've went back to the manual page.. For some reason I had the > impression cluster couldnt do this. thank you! > > ------------------------------ > *From:* FSL - FMRIB's Software Library [[log in to unmask]] on behalf of > Eugene Duff [[log in to unmask]] > *Sent:* 01 April 2017 22:47 > *To:* [log in to unmask] > *Subject:* Re: [FSL] Creating mask from localiser scan - selecting a > cluster / exclude others > > Hi Robert, > > Check out the cluster tool (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster) > - this should help you get want you want. > > Best > > Eugene > > On 31 March 2017 at 18:19, Rob Mok <[log in to unmask]> wrote: > >> Dear Experts, >> >> I'd like to make ROI masks based on a localiser scan. Using the >> uncorrected zstat images, I have clear clusters for the areas of interest, >> but there are also a lot of other clusters (sometimes large sometimes >> small) that I would like to exclude from this mask. >> >> I have done this before using the following command which takes all >> values above a threshold to make a mask (but the localiser mask I was using >> did not have other clusters at this threshold so was not a problem): >> >> fslmaths zstat1.nii.gz -thr 3.5 -bin output_mask.nii.gz >> >> I also know I can find the info about the clusters in an image by using >> the Cluster function. Could I select one of the clusters, either in FSL >> view or using some function (e.g. cluster) and create an ROI mask? >> >> Thank you >> Rob >> >> >> >