Thank you for your information. I think caret is really a huge
project.:-)
2009/4/1 Donna Dierker <do...@brainvis.wustl.edu>
Hi Jinhui,
Both Russ Poldrack (UCLA) and Morgan Hough (Oxford) were trying to do
something like this back in September, 2005. Here are a couple of
relevant threads, and there may be others of that vintage:
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00712.html
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00533.html
I don't know whether anyone eventually did anything like this, but I
doubt it. I can see attempting something like this with population
atlases (e.g., Harvard-Oxford Atlas on PALS_B12), but I'm not
anxious to
take on any more projects.
Colin really is the better target surface for AAL, which is based on
colin, rather than PALS_B12. The problem is that the 73730 standard
mesh
cortical surfaces are not included in the Caret distribution (and
finding them in sumsdb is easier said than done even for me). The
cerebellar 73730 mesh surfaces are included, but the cortical colin
surfaces are in the old Colin, hemisphere-specific meshes.
You can, of course, still map to these surfaces in your caret
distribution:
Human.colin.SPM2.LEFT.71785.spec
Human.colin.SPM2.RIGHT.71723.spec
But they won't work with the PALS_B12 standard visualization spec
files.
(The 73730 versions of these colin surfaces were registered from Colin
to PALS, and they do exist -- just not in your distribution.)
You could map the AAL volume, as a ROI paint volume, to the PALS_B12
surfaces directly (SPM2 or SPM5 -- probably very little difference).
But
colin differs from PALS_B12 anatomically in regions such as the IPL,
posterior left STS, etc. It doesn't feel valid to me.
No quick solutions, but stuff to keep in mind.
Donna
On 03/27/2009 10:09 AM, John Harwell wrote:
> How are you mapping the volume? To the PALS atlas or to an
individual?
>
> On what surface are you trying to view the results? Is it a PALS
> surface? If so, it will have the number 73730 (the number of nodes)
> in its name.
>
> You can also load the surface into Caret and then map the volume
using
> Map to Caret instead of Map to Atlas.
>
> -----------------------------------
> John Harwell
> j...@brainvis.wustl.edu
>
> Department of Anatomy and Neurobiology
> Washington University School of Medicine
> 660 S. Euclid Ave Box 8108
> Saint Louis, MO 63110
>
>
>
>
> On Mar 27, 2009, at 9:23 AM, Jinhui Wang wrote:
>
>
>> Dear John Harwell,
>> Thank you for your answers very much. AAL template is in the MNI
>> stereotaxic
>> space (here it is a nifti format of spm5).
>>
>> I have seen section 5.1 and tried every step as what the tutorial
>> tells.
>>
>> Following the suggestion in the tutouial, i don't run the mapping
>> algorithm and use the pre-computed ***.metric in the result/
>> subdirectory to view the result which is as a example. Everything
>> works. However, i also try to run the mapping algorithm to generate
>> new metric files and use them to view the reuslts. Unfortunately,
>> when i choose file/open data file and specify the new generated
>> metric files, a dialog box appear name "choose column to load"?
What
>> does this mean? And if i ignore it and press ok, an error happen
>> for the differnt number of nodes contained between the metric file
>> and the **coord file.
>>
>> God. Please give me a hand. ^_^
>>
>>
>> 2009/3/27 John Harwell <j...@brainvis.wustl.edu>
>>
>> Instructions on how to use the PALS atlas and how to map functional
>> volumes to the PALS atlas is available at
http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation
>> . Download the Caret 5.5 Tutorial - The Basics (including PALS
>> atlas). Section 5.1 contains instructions on how to map a
functional
>> volume to the PALS atlas surfaces. The human PALS atlas data set
is
>> available at http://sumsdb.wustl.edu/sums/humanpalsmore.do.
>>
>> I am not familiar with the AAL template. Do you know the
stereotaxic
>> space of AAL? Caret currently supports 711-2x, AFNI, FLIRT,
MRITOTAL,
>> SPM2, SPM5, SPM95, SPM96, and SPM99.
>>
>> Analyze files (hdr/img) typically lack the stereotaxic coordinate
>> information needed to map the volume to the surface.
>>
>> -----------------------------------
>> John Harwell
>> j...@brainvis.wustl.edu
>>
>> Department of Anatomy and Neurobiology
>> Washington University School of Medicine
>> 660 S. Euclid Ave Box 8108
>> Saint Louis, MO 63110
>>
>>
>>
>>
>> On Mar 26, 2009, at 9:41 PM, Jinhui Wang wrote:
>>
>>
>>> Hi,
>>> will you please give me some help on how to map AAL template (.img
>>> and .hdr; a public and used widely atlas) to PALS surface and
>>> display it. I have referred to some tutorial but don't solve it
>>> yet. Need i create some additional files?
>>>
>>> Sincerely
>>>
>>> --
>>> Jin-hui Wang
>>> State Key Laboratory of Cognitive Neuroscience and Learning,
>>> Beijing Normal University
>>> Add: No.19 Xinjiekouwai Street,
>>> Beijing, China. 100875
>>> Tel: +86 10 58802036
>>> Fax: +86 10 58806154
>>> E-mail: wjh...@gmail.com
>>> wjh122...@yahoo.com.cn
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users@brainvis.wustl.edu
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>> _______________________________________________
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>>
>>
>>
>> --
>> Jin-hui Wang
>> State Key Laboratory of Cognitive Neuroscience and Learning,
>> Beijing Normal University
>> Add: No.19 Xinjiekouwai Street,
>> Beijing, China. 100875
>> Tel: +86 10 58802036
>> Fax: +86 10 58806154
>> E-mail: wjh...@gmail.com
>> wjh122...@yahoo.com.cn
>> _______________________________________________
>> caret-users mailing list
>> caret-users@brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>
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--
Jin-hui Wang
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University
Add: No.19 Xinjiekouwai Street,
Beijing, China. 100875
Tel: +86 10 58802036
Fax: +86 10 58806154
E-mail: wjh...@gmail.com
wjh122...@yahoo.com.cn
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