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Hello everybody... I am trying to do some ROI analysis combining FSL and afni but flirt is giving me some unexpected results... here is what I am trying to do: afni has some predefined regions in TT space that I want to use for ROI analysis. In order ro use these ROIs I have to either transform them into my subject space or trasform my subject into TT space. I don't have very good quality subject images and transformation to TT space in afni is quite laborious so I have abandoned that approach. Another way would be to take the TT brain and find a transformation to subject space and apply that to the ROI map (to get the ROIs in subject space). But afni does not supply the TT brain. To go around that problem I have taken fsl standard brain and transformed it into afni TT space. Now I have a brain and ROI map in TT space to work with. Next, I wanted to use flirt to actually reslice the ROI map into my subject space. For that I first use flirt to find a transformation from my subject to the standard brain (in TT space). Then I find an inverse transformation that will take standard brain into subject space. And finally I apply that transformation to the roi map to get it too into subject space. That's where I get into a problem. I have 6 regions defined in my ROI map 3 on the left and 3 on the right side of the brain (left and right Brodmann's areas 17, 18 and 19). The map is the same size as the standard brain and the voxels have values 0 through 6 (0 is everything outside the ROIs). When I use flirt to reslice the map, I use '-interp nearestneighbour'. But when I look at the map, the colors are all over, meaning that I have values from 1 through 6 everywhere in the map (where I have expected to see 1 2 and 3 values only on the left and 4 5 and 6 on the right side). I have then tried to create a different map where I have only 2 regions - left and right only that I number 3 and 6. After the transformation I get an ROI map with values 1 through 6. Is it possible to use flirt and have it retain the values? In other words, if I have regions 1 2 and 3 on the left before transformation, that after transformation I would have only values 1 2 and 3 on the same side? I thought that's what 'nearestneighbour' would do, without actually changing the voxel values? should I do this some other way? sorry about this looong email and thanks for your help zrinka ps. here is the script that I run to do the transformation/reslicing: #find transformation matrix from hi-res to standard brain echo registration... /usr/local/bin/fsl/bin/flirt -in hook008-1-HiRes_brain -ref ../Atlas/FSLstandard+tlrc - omat HiResToStd.mat -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear #find the inverse transformation echo inverse transformation... /usr/local/bin/fsl/bin/convert_xfm -omat StdToHiRes.mat -inverse -matonly HiResToStd.mat #reslice the map using the transformation matrix calculated above (StdToHiRes.mat) echo reslicing... /usr/local/bin/fsl/bin/flirt -in ../Atlas/roi_visual+tlrc -out roi_visual_hook008-1 -ref hook008-1-HiRes_brain -applyxfm -init StdToHiRes.mat -interp nearestneighbour