Hello all<br><br>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&#39;s higher level statistic map back into the patients native space (high resolution) from standard space using Apply XFM in fsl.<br>


I have three questions regarding this:<br><br>1. The input is the transformation matrix that is found inside the feat director . My question is which transformation matrix &quot;standard2highres.mat&#39; should i use. Does it really matter if i used &quot;standard2highres.mat&#39; from run 1 rather than ran 2.<br>
<br>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 &#39;threshold.nii.gz&#39; file from the gfeat.directory.<br>
<br>3. What should the reference volume be? should this be the high resolution structural image ??.<br><br>Any help would be appreciated. <br><br>thanks<br>rajani<br>