Hi Tamir, I am assuming all registrations are “good” ( that is none of these differences are due to a failed registration ). For any transformation between images which isn’t equivalent to integer scaling between two perfectly aligned grids, there will be voxels which only have a partial overlap. For a binary mask, this will result in voxels in the transformed image having values in the range 0..1, this will almost certainly alter quantities such as non-zero volume of the mask. We usually partially account for this by thresholding-and-binarising the transformed mask at some value - this is typically 0.5, but the choice is somewhat arbitrary. Note that even a native-space "ground-truth” mask shouldn’t be expected to be same size for all subjects - some of the mask-size variation will be due to true subject anatomical variability. Hope this helps, Kind Regards Matthew -------------------------------- Dr Matthew Webster FMRIB Centre John Radcliffe Hospital University of Oxford On 1 Aug 2022, at 10:15, Tamir Eisenstein <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi FSL experts, I have three runs per subject acquired at the same session - two resting state and a task, which have the same spatial and temporal resolutions. I created a mask from a cluster of activation from the task group-level analysis and wanted to transform it from standard to native space for each of the three runs in each subject. However, for each run in the same subject, I get a slightly different transformed mask with different number of voxels. In addition, for different subjects I get significantly different masks in terms of voxels number - isn't a specific MNI mask transformation to different native spaces suppose to yield the same native-space mask in terms of voxels number across all subjects? I have followed the instructions on the web to conduct the invert transformation (with my own paths and file names of course): invwarp -w highres2standard_warp -o standard2highres_warp -r highres applywarp -i activationMaskMNI -r example_func -o activationMaskNative -w standard2highres_warp --postmat=highres2example_func.mat I would very appreciate any insights, Many thanks, Tamir ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/