Hi,



If things are aligned in FSLView but not in SPM’s check_reg then I think this might be more of an issue related to SPM, and you might have more luck on the SPM list.



If you want to get your EPI aligned to the MNI space using SPM, then I assume there will be SPM functions that could apply the DARTEL transformation to the EPI and give you what you want.



All the best,

	Mark



> On 11 Dec 2014, at 14:53, Alexander Taylor <[log in to unmask]> wrote:

> 

> Hello Experts,

> 

> I am trying to use a DARTEL template (as I have a dementia based population) in my pipeline of preprocessing and registration using FSL's FEAT as the main tool for this. I currently run my prestats (motion correction, B0-warping and Smoothing) in FEAT (using native T1 image only for coregistration of the EPI).  I then plan to start the pipeline a new and input my T1 DARTEL warped subject image as the Highres image for a new coregistration step and then finally to MNI space.

> 

> So firstly the starting point of fsl prestats and DARTEL template creation is the same T1 images. The problem I am having is that when I overlay the preprocessed EPI image on to the original T1 image they do not align in SPM Check_Reg viewer, but do align in FSLview. I am aware that this maybe a header issue between FSL and SPM. So I have tried to use the following command to resolve the issue: 

> 

> flirt -in EPI -ref T1 -applyxfm -usesqform -out EPI_new

> 

> The result of this however, is an image even more misaligned.

> 

> So what I am trying to achieve is a way to transform my preprocessed EPI image into the same position as the T1 image, to ensure when I input my DARTEL template as the main T1 image for the next step of my pipeline they start in the same position, so that FSL does not try to estimate another transformation.

> 

> Finally, if anyone has tried to successful use DARTEL in an FSL pipeline previously any other suggestion on how to go about this would be much appreciated.

> 

> Many Thanks

> Alexander Taylor