[caret-users] Target space

[Donna Dierker]

Hi Jackie,

See inline replies below.

Donna

On 08/30/2007 08:43 AM, Chuan-Chih Yang wrote:
> Hi Donna,
>
> Thanks again for the suggestions. I decide to chagne to PALS_B12.
> Is there an PALS_B12 dataset that are in native space (structural volume
> scans)? 
>   
Technically, yes, those scans exist and may be part of the OASIS dataset 
available from Dan Marcus.  But the anatomical volumes used to generate 
the PALS_B12 surfaces were originally multiple (3-4) MPRAGES 
coregistered, averaged, and written to 711-2C atlas space in a single 
resampling, using Avi Snyder's imgreg.  The PALS_B12 surfaces were 
generated from the resulting atlas space MPRAGE, and these surfaces were 
subsequently registered to various atlas spaces using the procedures 
defined here:

http://brainvis.wustl.edu/help/pals_volume_normalization/
> I wanna use Freesurfer to generate the surface version of PALS_B12, and then
> cut & flatten the patches, 
Why?  I'm afraid I'm completely lost on what you're trying to do.
> and then use CARET to do the landmark-based
> warping. (I would like to select some landmarks on the individual patch & on
> the PALS_B12 patch)
>   
Many people use Freesurfer to segment their volumes and generate 
surfaces, and then use Caret to register those surfaces to the PALS 
atlas.  But it almost sounds like you're trying to recreate the PALS 
atlas using Freesurfer-generated surfaces, and this goal confuses me.  
I'm pretty sure Fischl, et. al., have put the OASIS dataset through 
Freesurfer processing stream, so the PALS surfaces probably do exist in 
Freesurfer form somewhere, but you would need to consult Dan Marcus or 
Fischl et. al. on getting those surfaces and establishing correspondence 
between the OASIS ID's and the Buckner case numbers.

I'm probably misinterpreting your intent, so please clarify your goal.
> Cheers,
> jackie
>
>
>
>
>
> Am 29.08.2007 15:12 Uhr schrieb "Donna Dierker" unter
> <donna at brainvis.wustl.edu>:
>
>   
>> Hi Jackie,
>>
>> See inline replies below.
>>
>> Donna
>>
>> On 08/29/2007 07:16 AM, Chuan-Chih Yang wrote:
>>     
>>> Dear list,
>>>
>>> I got a question about the selection of target space (mapping volumes onto
>>> surface). My attemp is to map the functional zstat.nii of FSL onto N27
>>> template by using caret. I found different target spaces that I can choose
>>> from in the 'atlas surface selection' window,
>>>   
>>>       
>> I hope you have a good reason for selecting Colin as the target surface,
>> rather than PALS_B12.
>>     
>>> in my case--- the zstat of individual in not yet normalized to any space,
>>> but the group zstat is already normalized to MNI 305,by FLIRT. I am
>>> wondering which target space and altas shall I choose, if I wanna normalze
>>> the zstat from FSL onto N27?
>>>   
>>>       
>> We don't have a version of Colin that was normalized using FLIRT (linear
>> affine), but we do have versions of colin in SPM99 and SPM2 space.  (See
>> http://brainvis.wustl.edu/help/pals_volume_normalization for an
>> explanation of how methods and spaces relate in our terminology.)  You
>> could use one of these for your group results, but I'd really recommend
>> using the PALS_B12 FLIRT surface as your mapping target for those group
>> results.
>>
>> For your non-normalized individual results, you really can't use any of
>> our atlas targets -- colin or PALS_B12.  If you want to map the native
>> individual results, you'll need to segment his/her structural volume and
>> map to the individual's surface.
>>     
>>> Is there any difference between mapping the individual zstat and the group
>>> zstat from FSL onto N27?
>>>       
>> Absolutely:  Mapping individual results to colin -- even normalized
>> results -- is a bad idea.  Even mapping normalized individual results to
>> PALS_B12 surface isn't a great idea.  Mapping individual results to its
>> own surface reconstruction is a good idea.
>>
>> Mapping group results to colin is no longer recommended, because of the
>> limitations inherent in a single subject target.  Colin has strange
>> anatomy in some places that cause undesirable mapping results in some
>> areas (e.g., left posterior STS and IPL).
>>
>> Mapping group results to PALS_B12 is the recommended option.
>>
>> If you're interested in seeing how the individual's results differ from
>> the group's, then I can think of two ways to accomplish this, but please
>> be advised that I'm not experienced in these kind of analyses, so I
>> don't know if a reviewer would be happy with them:
>>
>> * Normalize your individual to the same target used for your group
>> results.  Compute the difference in volume-land.  Map the difference
>> volume to the PALS_B12 FLIRT surface.  Consider using the MCW BrainFish
>> algorithm.
>>
>> * Normalize your individual to the same target used for your group
>> results; reconstruct your individual's surface; map the individual zstat
>> to the individual's surface; and register it to PALS_B12.  Map the group
>> zstat to the PALS_B12 FLIRT surface.  Use Attributes: Metric:
>> Mathematical Operations to subtract one from the other (or
>> caret_command's new metric math, if you have the latest and greatest
>> command line utility).
>>
>> Either way, you're guaranteed to get lots of clusters of differences;
>> however, I'm not sure how you'd establish significance criteria.  Any of
>> the 12 Buckner subjects that contributed to PALS_B12 will have such
>> clusters where its individual surface differs from the PALS_B12 group
>> target (i.e., normal anatomical variability is pretty high in humans).
>>     
>>> (is there a availble N27 altas that is FLIRTed into
>>> MNI305 ? )
>>>   
>>>       
>> No.  You may have a good reason for using Colin, but I'd like to know
>> what it is.
>>     
>>> Thanks much for the help!
>>>
>>> Cheers,
>>> jackie
>>>