Hi Donald,
I don't see any way to just warp the data. What you really want to know
in your example is what the Harvard-Oxford labels would have been had they
been derived using registrations that involved FNIRT. That seems an
empirical question to me. Ideally, one would want to use a set of ROIs
derived using the same templates and algorithms as the study to which
those ROIs are going to be applied. But since that isn't always possible
you have a make a decision informed by the needs/questions of your
particular study.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 11/28/12 1:24 PM, "MCLAREN, Donald" <[log in to unmask]> wrote:
>Michael,
>
>Excellent points. However, the underlying question still remains about
>using existing ROI with newer normalization approaches.
>
>For example, would using the Harvard-Oxford labels be bad if you use
>FSLs FNIRT as they were created with FLIRT? Or is there a way to warp
>the data?
>
>We are not using DARTEL, just SPM's regular non-linear warp.
>
>On Wed, Nov 28, 2012 at 1:50 PM, Michael Harms <[log in to unmask]>
>wrote:
>> I would think that you might raise some eyebrows using ROIs obtained
>>using
>> FSL's FLIRT in data normalized using SPM's non-linear (Dartel?) tool,
>>due
>> to the big potential difference between linear (affine) and non-linear
>> approaches. Of course, it would depend on the anatomical precision that
>> you want/need for your particular study and whether the ROIs involve
>> regions that are particularly sensitive to non-linear registration.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> -----------------------------------------------------------
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO 63110 Email: [log in to unmask]
>>
>>
>>
>>
>> On 11/28/12 11:43 AM, "MCLAREN, Donald" <[log in to unmask]>
>>wrote:
>>
>>>Dear SPM/FSL users,
>>>
>>>It seems that there are several templates (SPM v FSL) as well as
>>>different normalization routines that could result in slight
>>>variations of the localization of the results. Do I need to worry
>>>about these small differences between methods?
>>>
>>>In particular, I want to know if I can take regions defined in a study
>>>using FLIRT in FSL and use them in my study that has been processed
>>>with SPM's non-linear normalization tool. Can I use them as is or is
>>>there a transform that can I compute and/or apply to the ROIs to get
>>>them into the SPM normalized space.
>>>
>>>Thank you in advance for your input.
>>>
>>>Best Regards, Donald McLaren
>>>=================
>>>D.G. McLaren, Ph.D.
>>>Research Fellow, Department of Neurology, Massachusetts General Hospital
>>>and
>>>Harvard Medical School
>>>Postdoctoral Research Fellow, GRECC, Bedford VA
>>>Website: http://www.martinos.org/~mclaren
>>>Office: (773) 406-2464
>>>=====================
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