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
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