Hi,
I posted this question before but did not recieve any replies. I would greatly appreciate any help. 

While pre processing, after the normalization step, when I use check reg for viewing results I noticed there is a shift in the images so that the scans are no longer aligned (I changed the parameter file as was offered bellow). Also  it seems that part of the occipital lobe is cut out. Then I tried to take out the segmentation and indirect normalization and only normalized using the EPI template and still the same shift. 
I attached an image- with m.structural.img, functional.image, r.functional, wr.fuctional and swr.functional. It is visible that the realignment and coregistration are ok. The images move after the normalization which was done as described in my previous question below-using the segment: Norm Params Subj->MNI as parameter file.
Why does this occur? How can I fix this?
Thanks
Abigail

>
This is where it went wrong:
    Normalise: Write: for Parameter file used: DEP Realign:
Realignment Param File.
Instead, you should use the deformations estimated by the Segmentation.
Best regards,
-John
On 11 January 2012 13:03, Abigail Livny-Ezer <[log in to unmask]> wrote:
> Hi
> I am trying to run a preprocessing batch but received an error on the normalization module. I am not sure what I did wrong.
> The stages I ran are:
> 1.      Realign: Estimate & Reslice
> 2.      Coregister: Estimate: using the mean image as the reference and my 3D structural as source images.
> 3.      Segment: DEP coreg: Estimate: Coregistered Images.
> 4.      Normalise: I wanted to normalize both functional and structural images therefore I entered 2 normalise modules:
> -       Normalise: Write:
> for Parameter file used: DEP Realign: Realignment Param File.
> for the images to write used: DEP Realign: Resliced images.
> -       On the second normalise module I used
> for Parameter file: DEP Segment: Norm Params Subj->MNI.
> for the images to write used: DEP Segment: Bias Corr Images.
> I believe this is where I get an error message.
> What did I do wrong?
>
>  For a second group of patients with brain lesions I would like to use the cost-function masking. I understand I need to create a mask using MRICron on all slices and then add to the normalize module. How do I do this? Where is there an option to add a mask to normalization and do I then only use the normalization of the functional images?
> I have read a few refs on this topic (Brett et al. 2001, Anderson et al. 2010), but can use more practical advice on how to do this.
>
> Thanks
> Abigail