[caret-users] question for caret

[John Harwell]

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
john at 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 <john at 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
> john at 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:  wjhmjy at gmail.com
> >            wjh122122 at yahoo.com.cn
> > _______________________________________________
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> > caret-users at 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:  wjhmjy at gmail.com
>            wjh122122 at yahoo.com.cn
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