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Dear Niels, I also tried the Nudge gui, it is greatly convenient, but seems can not load the fslview and my teminal said :"sh: 1: /usr/local/bin/fslview: not found ". Can I do something here? Thanks, Kaiming On Fri, Jun 20, 2014 at 11:39 AM, Kaiming Yin <[log in to unmask]> wrote: > Hi Niels, > > thanks for the suggestion, I am trying to use the makerot to generate the > rotation matrix, and the convert_xfm to concatenate the matrix together. > However, I am not sure how is the rotation going. Because I am rotating > using the Euler angles on ZXZ-axises. and angles can be like e.g. phi=30, > theta=45, tau=0. Could makerot generate this matrix? > > Thanks, > Kaiming > > > On Thu, Jun 19, 2014 at 3:07 PM, Niels Bergsland <[log in to unmask]> > wrote: > >> The tool Nudge can also help you create the transformation matrix (it >> will also call flirt). >> >> On Thu, Jun 19, 2014 at 3:49 PM, paul mccarthy <[log in to unmask]> >> wrote: >> > Hi Kaiming, >> > >> > The 'flirt' command allows you to specify an affine transformation >> matrix to >> > apply to an image. So if you create an affine transformation with your >> > desired rotations, and save it as a plain text file (e.g. >> 'rotate.mat'), you >> > can apply it to an image (e.g. 'image.nii.gz') like so: >> > >> > flirt -in image.nii.gz -ref image.nii.gz -applyxfm -init affine.mat -out >> > rotated.nii.gz >> > >> > Cheers, >> > >> > Paul >> > >> > >> > On Thu, Jun 19, 2014 at 2:18 PM, Kaiming Yin <[log in to unmask]> >> > wrote: >> >> >> >> Hi guys, >> >> >> >> can FSL help with a random rotation of the MR image? e.g. a rotation >> of 30 >> >> degree in X-axis, 90 in Y-axis, and 120 in Z-axis. >> >> >> >> Thanks in advance, >> >> Kaiming >> > >> > >> >> >> >> -- >> Niels Bergsland >> Integration Director >> Buffalo Neuroimaging Analysis Center >> 100 High St. Buffalo NY 14203 >> [log in to unmask] >> > >