Hi,
If you can't overlay the results then the transformation has not worked.
Look at the sizes of the images with fslsize for the structural image
and the transformed statistical image. They should be the same.
If the structural image was used as the reference image then the
output of the applyxfm will definitely be that size, so I'm guessing
that this hasn't been done correctly.
All the best,
Mark
rajani sebastian wrote:
> The transformation worked fine but now i have trouble viewing the
> image on FSL view. I want to overlay the transformed statistics image
> on the subjects high resolution image, but when i do that i get this
> error message " unable to load incompatible overlay. all overlays must
> have same dimensions as the base image".
> I am not sure why this happens.
> thanks
> rajani
>
> On Tue, Mar 24, 2009 at 8:34 AM, rajani sebastian
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> thanks!!!
>
>
> On Tue, Mar 24, 2009 at 4:00 AM, Mark Jenkinson
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> If you are using the same highres image in each case then
> there should
> be no difference between the standard2highres.mat files.
>
> If you want to transform your statistics, then the statistic
> images are the
> input images. If you've done cluster correction it is
> probably best to
> transform the thresholded statistics rather than the
> unthresholded ones.
> Do not transform the rendered ones though - stick to the
> thresholded
> stats.
>
> As for the reference volume - it needs to be the highres image
> if that
> is the space that you want the statistics to end up in.
>
> All the best,
> Mark
>
>
>
>
> On 23 Mar 2009, at 19:18, rajani sebastian wrote:
>
> Hello all
>
> My experiment consists of three runs of the same task in
> patients with brain lesion. Initially, i analyzed data
> from all the three runs separately and then used higher
> level analysis using fixed effects to combine the three
> runs. Now i want to register each patient's higher level
> statistic map back into the patients native space (high
> resolution) from standard space using Apply XFM in fsl.
> I have three questions regarding this:
>
> 1. The input is the transformation matrix that is found
> inside the feat director . My question is which
> transformation matrix "standard2highres.mat' should i use.
> Does it really matter if i used "standard2highres.mat'
> from run 1 rather than ran 2.
>
> 2. What should the input volume be? I wanted to be able
> to register the higher level statistics map back to the
> subjects native space. So should this be the
> 'threshold.nii.gz' file from the gfeat.directory.
>
> 3. What should the reference volume be? should this be the
> high resolution structural image ??.
>
> Any help would be appreciated.
>
> thanks
> rajani
>
>
>
