Re: [caret-users] Re: Deforming borderprojection files - macaque to PALS registration

Tue, 16 May 2006 21:54:16 -0500 

Terry et al.,
Donna's evaluations and recommendations regarding registration of the macaque to the PALS atlas are on track - it can indeed be done by a two-step procedure using existing deformation_map files. 


However, this brings home the point that it makes more sense to do a  
direct registration between the macaque atlas and the PALS atlas,  
without using Colin as an intermediary.  This has been on my 'to-do'  
list for quite a while; your inquiry will hopefully bump it up in  
priority.  Once it is done, I will send an email to caret-users about  
where to access it in SumsDB.



For the record, my expectation is that the differences in one-stage  
vs two-stage registration from macaque to PALS should be very small.   
The common substrate will be the landmark borders drawn on the Colin  
flat map.  For the PALS registration, the plan is to (i) start with  
the landmark borders projected to the Colin flat map; (ii) save the  
border points as a 'border file' (preserving locations on the map  
without an associated topology file); (iii) open this newly created  
border file while viewing the PALS-resampled version of the Colin  
flat map; (iv) project the landmark borders to the PALS (73,730-node)  
atlas; (v) register the macaque to PALS using the PALS spherical  
map.  You're welcome to try this on your own if you want.


David


On May 13, 2006, at 5:14 PM, Terry Sewards wrote:


Hi Donna,

As soon as I put the correct file locations in the deform_map file the

deformation (macaque to Colin) worked fine.  I imagine the same  
will be true

in going from Colin to the PALS atlas.  Thanks!

Terry

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Today's Topics:

   1. Re: Deforming borderprojection files (Terry Sewards)
   2. Re: Re: Deforming borderprojection files (Donna Dierker)



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Message: 1
Date: Fri, 12 May 2006 09:48:24 -0600
From: "Terry Sewards" <[EMAIL PROTECTED]>
Subject: [caret-users] Re: Deforming borderprojection files
To: <caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"

Hi,


I've been trying to deform *.borderproj files from the PALS Atlas  
to the
Macaque Atlas (and vice versa), but I'm having trouble figuring  
out the
procedures involved.  Do I have to deform to the Colin atlas  
first, and

how

is this done?  Does it require flat surface deformation, and if so is

there

a goaround for the Windows version?  Thanks in advance.

Terry Sewards


------------------------------

Message: 2
Date: Fri, 12 May 2006 11:54:01 -0500
From: Donna Dierker <[EMAIL PROTECTED]>
Subject: Re: [caret-users] Re: Deforming borderprojection files
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Terry,

You're in territory I fear to tread.  I've never done a cross-species

registration myself, but in theory it's doable. Like you, I'm  
guessing
the route from PALS_B12 to F99UA1 will be through Colin.  If you  
search
http://sumsdb.wustl.edu/sums/index.jsp for filename F99UA1 and  
file type

deform_map, the most recent entries are from 2004 (probably the Denys
and Orban papers), which used colin for the human target.


There are Colin <-> PALS_B12 deform_maps in sumsdb, so you could  
deform

a file in two steps:  Once from PALS to colin, then from colin to
F99UA1.  Once you get the deformation maps, then you can use Surface:

Deformation: Apply Deformation Map on your borderproj file.   
You'll have
to change the source and target directories, since they won't  
match your

file system pathnames.


Flat registration shouldn't be required; in fact, registration  
shouldn't

be required.  It's just a matter of hunting down the right deform_map
files in sumsdb; making sure you have all the F99UA1, Colin, and
PALS_B12 files those deform_map files need; and applying them in the
right polarity/sequence.

Give it a go on your own, and if you get stuck, let us know.  David's
the real cross-species expert (hope that doesn't come off wrong), but
he's in Seattle and heads to Japan next week.

On 05/12/2006 10:48 AM, Terry Sewards wrote:


Hi,


I've been trying to deform *.borderproj files from the PALS Atlas  
to the
Macaque Atlas (and vice versa), but I'm having trouble figuring  
out the
procedures involved.  Do I have to deform to the Colin atlas  
first, and

how

is this done?  Does it require flat surface deformation, and if  
so is

there

a goaround for the Windows version?  Thanks in advance.

Terry Sewards

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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see

http://home.att.net/~donna.hanlon for details.)



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