And sorry, I forgot to ask.

Is there a possibility to take out only the brain from subjects,
instead of normalizing the whole skull. Something like skull-stripping
can be normal, or maybe a re-combination of gray and white matters
(c1/c2) in gray and white colors. This would be much more easy to
render in 3d in, for example, MRICroN.

Thank you
Dorian.

2009/6/17 Dorian P. <[log in to unmask]>:
> 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
>> reader of the e-mail is not the intended recipient or the employee or agent
>> responsible for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and privileged
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>>
>