Hi,
As far as I know, SPM stores the transformation in the header but does
not apply it to the image data itself. Therefore, you do not see changes
when opening with FSLview. You might need to reslice the data in FSL in
order to store image data with the transformations applied.
In FSL, I prepare the data with fslswapdim to get it roughly oriented in
a way my reference image is oriented. Then I use flirt to co-register to
a reference template. For structural MRI data I prefer the INIA19
template (https://www.nitrc.org/projects/inia19), but when using DTI
data, it might be worth to check out the DTI teplate:
https://www.nitrc.org/projects/rmdtitemplate
If I really want to manually rotate images, I prefer using the mango
tool (http://ric.uthscsa.edu/mango), it has a nice interface for
applying rotations and translations (menu -> Image -> Transformations).
So far it seems to work well together with FSL.
I hope this helps,
wolf
On 12/11/2015 11:48 AM, Dominik Biezonski wrote:
> Dear FSL community,
>
> I am working on a monkey (macaque) DTI dataset. The issue is that each brain was scanned ex vivo in random orientations, such that the resulting brains are randomly rotated when I open them in FSLview. I need assistance in manually rotating each brain so that I can run registration steps through TBSS on properly oriented images. I've tried using SPM to do this, which when you save and open again in SPM seems to work, but when you open these seemingly "reoriented" images in FSL, they look like the originals - randomly oriented. I tried using Nudge_gui but there doesn't seem to be an option to save the manually rotated images. I've also tried using fslorient to play with the q- and s-form codes, to no avail. Do you have any suggestions on how I can manually rotate these brains in space for my analysis? Seems like such a trivial thing, but with no means to do it.
>
> Thank you so much for your time and input,
>
> Dom
>
> Dominik Biezonski, Ph.D.
> Assistant Professor in Psychiatry
> Columbia University - NYSPI
> 1051 Riverside Drive, Rm. 2420
> New York, NY 10032
> 646-774-5879
> [log in to unmask]
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