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
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