On Tue, Mar 24, 2009 at 4:00 AM, Mark Jenkinson
<[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
