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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