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Subject:

DARTEL normalization of fMRI data

From:

Mike <[log in to unmask]>

Reply-To:

Mike <[log in to unmask]>

Date:

Wed, 27 Jul 2016 21:18:27 +0100

Content-Type:

text/plain

Parts/Attachments:

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text/plain (37 lines)

Hi DARTELers,

Because my subjects are aged patients with possible brain structural changes, I want to perform DARTEL normalization rather than default spatial normalization in SPM8 so as to have a better spatial normalization.

All EPI images were adjusted for timing differences between slices, unwarped using field maps, realigned and re-sliced to correct for motion artifacts (producing rxxx.nii). The resulting mean EPI was co-registered with the subject's T2-weighted image, which in turn was aligned with the T1-weighted image (that is, T1WI has been coregistered to EPI). 

Below is my procedure for DARTEL normalization and I hope someone could help to confirm my procedures:

(1). Segment
  Images = Coregistered T1WI
  Grey matter/white matter/CSF = Native space
  [This process produced a xxx_sn.mat file as well as c1xx, c2xx, c3xx files corresponging to GM, WM, and CSF]

(2). DARTEL tool, Initial import  
  Parameter files = xxx_sn.mat  
  GM, WM, CSF: Yes
  Voxel size: 1.5
  [This process produced rc1xx, rc2xx, rc3xx file]
 
(3). DARTEL tool, run DARTEL
  Images: rc1xx, rc2xx, rc3xx
  [This process produced u_rc1xx, u_rc2xx, u_rc3xx file, and a series of template files, with the last one called template_6.nii]

(4). Normalize into MNI space 
  DARTEL template: template_6.nii
  Few subjects            
    Flow fields = u_rc1xx
    Images = rxxx.nii
  Preserve = Preserve Concentrations ("no modulation") 
  [This process produced swrxxx.nii but also Template_6_2mni.mat]

Are my procedures correct? 
However, the voxel size in swrxxx.nii is 1.5x1.5x1.5. If I want to get a MNI standard space with 2x2x2 voxel size, how should I do?
Also, (4) performed not only normalization but automatically smoothing process...          

Thanks in advance. Mike

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