Make sure that the parts of the brain that are missing in your
spatially normalised images are present in all of your original scans.
If the data was not within the original FoV, it will not exist in the
spatially normalised data.
Best regards,
-John
On 23 January 2012 19:55, Raveendran, Janani A.
<[log in to unmask]> wrote:
> Hi,
>
> In pre-processing resting-state data using SPM8 with DARTEL, I ran into spatial
> normalization problems with a few of our subjects. I've attached the normalized
> realigned, slice-time corrected image for one of these subjects (i.e.
> wrarest_brain.nii). As you can see, whole parts of the brain are missing, and
> that should not be the case. Below is the batch I used to pre-process this data.
> What might be the problem?
>
> Thank you,
> Janani
>
> Batch:
> 1.Named directory selector
> 2.Change directory
> 3.Slice timing
> a. Data: Session: raw functional data (i.e. 'rest_brain.nii' files)
> 4.Realign: Estimate and Reslice
> a. Data: Session: Slice Timing Corr Images**
> 5.Coreg: Estimate
> a.Reference image = Estimate and Reslice: Mean Image**
> b.Source image = Structural image
> 6.Check Reg
> a.Images: Coreg: Coregistered images**
> 7.Segment
> a.Images = Coreg: coregistered images**
> b.Grey matter/white matter/CSF = Native space
> 8.Initial import
> a.Parameter files = Norm Params: Subj --> MNI**
> b.Output directory = same directory as above
> 9. Run DARTEL
> a.Images: imported tissue (GM)**
> b.Images: imported tissue (WM)**
> 10.Normalize into MNI space
> a.DARTEL template = template_6.nii**
> b.Few subjects
> i.Flow fields = flow fields**
> ii.Images = c1 images** (grey matter only)
> c.Preserve = Preserve Concentrations ("no modulation")
> 11.Normalize: Write
> a.Parameter files: Norm Params: Subj --> MNI**
> b.Images to write: Estimate and Reslice: Resliced images (Sess 1)**
> c.Voxel size: [2 2 2]
> d.Interpolation: 7th degree B-spline
> 12. Smooth (functional data)
> a.Images: normalized images (Subj 1)**
> b.Voxel size = [6 6 6]
>
> ** dependency
>
>
>
>
>
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