[caret-users] Mapping BrainVoyager statistical volumes to PALS atlas

[Donna Dierker]

... this time to the list, so John knows I'm on it.

-------- Original Message --------
Subject: 	Re: [caret-users] Mapping BrainVoyager statistical volumes to 
PALS atlas
Date: 	Tue, 02 Dec 2008 07:32:17 -0600
From: 	Donna Dierker <donna at brainvis.wustl.edu>
To: 	Manny Vindiola <mannyv at gmail.com>
References: 	<9e7065220812011621w4af004bfyf145c6868690d1af at mail.gmail.com>



Hi Manny,

Back in the old SureFit and Map2Surface days, it was important to 
resample the functional volume in the same grid as the anatomical volume 
used to generate the surface.  In Caret, this is no longer the case.  
Assuming your functional volume's origin is the intersection of the 
ACsup and ACpost 
(http://afni.nimh.nih.gov/pub/dist/edu/latest/afni10_volreg_talairach/afni10_volreg_talairach_files/Slide0021.gif), 
then it should align without further preprocessing.

Please do upload your NIfTI anatomical and functional volumes here:

http://pulvinar.wustl.edu/cgi-bin/upload.cgi

I don't think I can take BV files directly.

I will determine whether your volumes align with each other, as well as 
whether they align with the PALS AFNI+tlrc average fiducial surfaces.

Donna

On 12/01/2008 06:21 PM, Manny Vindiola wrote:
> Donna,
>
> Thanks for your reply. I to am hoping that I can massage the BV files
> so that I can use the AFNI surface as a proxy. Here is some
> information regarding the functional and statistical formats BV uses
> for a talairached dataset.
>
> The data sits in a bounding box around the anatomical with dimensions:
> 139 x 175 x 121
>
> According to one of the mapper help files the AFNI talairach grid is:
> 161x191x151
>
> I don't know if there is a straight forward way to adjust the BV files
> to enlarge the bounding box. Obviously I can zeropad the file but I am
> not sure that will have the appropriate effects. Would it help if I
> uploaded an anatomical and functional image for you somewhere?
>
> thanks for your help,
> Manny
>
>   
>> Hi Manny,
>>
>> I have no Brainvoyager experience, but I map NIfTI to PALS often.  Which
>> version of Caret are you running?  John Harwell fixed some NIfTI issues
>> a while back, but I don't recall exactly when.  If you are using the
>> most recent version (Version 5.61 - 12 November 2008), then those
>> changes should be incorporated already.
>>
>> The volume issue must be resolved before the next issue can be
>> pinpointed:  Why isn't the AFNI surface a good proxy for Brainvoyager,
>> since both packages use the Talairach & Tournoux 1988 (T&T88) recipe for
>> spatial normalization?  Or at least they used to; I'm guessing most AFNI
>> users now use @auto_tlrc to spatially normalize their subjects.  While
>> it still uses the T&88 bounding box / scale, it uses an affine transform
>> to get there, rather than the piecewise linear process defined in
>> T&T88.  I do not know whether Brainvoyager now offers an affine option;
>> however, the PALS AFNI surfaces were normalized using the old, manual
>> method, because the affine option did not exist when these surfaces were
>> created.
>>
>> If it is really true that the PALS AFNI surfaces are poor proxies for
>> Brainvoyager, then we will need to consider developing Brainvoyager
>> surfaces.  But I would like to see some evidence before adding that task
>> to our queue.
>>
>> Donna
>>