Dear all (and John and Donald),
I managed to understand how to do a good normalization. But apparently
there are many options, and the Dartel guide is getting me confused.
Method 1 - segment only
New Segment (spm8) -> use deformation fields to normalize (y_*).
Method 2 - segment and Dartel
New Segment (spm8) -> create template in Dartel (Template_6.nii) ->
->(a) (section 34.2.1 in manual)
normalize template in SPM -> combine deformation from normalization of
template (*_sn) and individual individual match to template (u_rc1*)
-> apply this deformation to original T1
->(b) (section 34.1.4 in manual)
normalize to MNI in Dartel -> ... ??? (this creates "smwrc1/smwrc2" files).
The first two methods I could run (1 and 2a), but John's advise to use
Jacobian determinants applies only to the 2(b), which I don't know how
to finish. "smwrc1/smwrc2" files are gray and white matter and no
deformation field is produced by Dartel when normalising to MNI space.
If that deformation exist I can immagine a combination with the
individual template warp (u_rc1*) will give the final deformation.
Maybe I am asking too much, but as I am here, I want to understand the it all.
P.s. The template creation in Dartel produced
"Template_1/2/3/4/5/6.nii" in the first subject directory. Hope this
is normal.
2009/6/15 MCLAREN, Donald <[log in to unmask]>:
> DARTEL works pretty well. You just need to apply the flow fields to the T1
> images after you compute them from the segments. Then average the normalized
> images.
> If you don't want to use a gaussian smoothing kernel, then use a median
> filter in matlab. A median filter will retain the edges better than gaussian
> smoothing.
>
> On Mon, Jun 15, 2009 at 9:43 AM, Dorian P. <[log in to unmask]> wrote:
>>
>> Yes Donald, mean of all subjects.
>>
>> Thank you.
>>
>> 2009/6/15 MCLAREN, Donald <[log in to unmask]>:
>> > "mean" for a single subject or "mean" of a group?
>> >
>> > On Mon, Jun 15, 2009 at 4:52 AM, Dorian P. <[log in to unmask]> wrote:
>> >>
>> >> Dear all,
>> >>
>> >> I asked briefly in another thread, but couldn't have a clear response.
>> >>
>> >> What is the best way to perform a good normalization on structural MRI
>> >> in order to produce a "as-sharp-as-possible" mean T1 image? Is it the
>> >> new segmentation from SPM8, Dartel, or normal segmentation can work
>> >> equally well (i.e. in SPM5)?
>> >>
>> >> In case SPM8 or Dartel is better, can somebody help with a few
>> >> instructions on how to do the normalization exactly?
>> >>
>> >> Thanks a lot.
>> >> Dorian.
>> >
>> >
>> >
>> > --
>> > Best Regards, Donald McLaren
>> > =====================
>> > D.G. McLaren
>> > University of Wisconsin - Madison
>> > Neuroscience Training Program
>> > Office: (608) 265-9672
>> > Lab: (608) 256-1901 ext 12914
>> > =====================
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>
>
> --
> Best Regards, Donald McLaren
> =====================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Office: (608) 265-9672
> Lab: (608) 256-1901 ext 12914
> =====================
> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
> intended only for the use of the individual or entity named above. If the
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