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Hi Ruifeng, FLIRT will preserve orientation labels when registering/transforming an image - if the orientation of the FLIRT/FAST output is incorrect, then this suggests that the orientation of the input is incorrect. Are the orientation labels correct for both of your raw images? If not, then you need to fix this before performing any processing. You can find some information on this problem here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained Paul On Tue, 23 Aug 2022 at 15:57, Ruifeng Dong <[log in to unmask]> wrote: > Hi all, > > I am a new user of FIRST. > > I am trying to do brain segmentation using FIRST. My data came from two > scanners. One uses LPI orientation and the other uses RAI. The subcortical > structure volumes look fine for LPI images, but apparently wrong for RAI > ones. See attached. Then I flipped the RAI images using fslreorient2std and > the volumes look fine again. This seems ok, but how do we know whether the > left and right are flipped during the registration, as they are roughly > symmetric? (*Question 1*) > [image: image.png] > > I then tried to dig deeper. I registered the two images using FLIRT and > MNI152_T1_1mm.nii.gz. Again the AP and LR directions are wrong for the RAI > images. See attached. Is this caused by the initial value of rotation > matrix chosen in FLIRT? If so, can we just manually set it to solve this > issue? (*Question 2*) > A slice of registered RAI image: > [image: image.png] > > The slice in MNI152: > [image: image.png] > > Thank you! > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 > ######################################################################## 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/