[caret-users] question for caret aka mapping AAL to PALS/colin

Wed Apr 1 07:16:16 CDT 2009

Jinhui,

The 73730-node (standard-mesh) colin surfaces are accessible in  
SumsDB.  If you want just the coordinate files, select:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6154943
(archive_name=Human.colin.R.RegToPALS_B12.LR.FIDUCIAL.TLRC.711-2B. 
71723.coord)
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6154882
(archive_name=Human.colin.L.RegToPALS_B12.LR.FIDUCIAL.TLRC.711-2B. 
73730.coord)

If you want a well-configured spec file that includes inflated and  
flat surfaces and the colin sulcal depth file, go to the directory:
http://sumsdb.wustl.edu/sums/directory.do?id=6163834&dir_name=COLIN_RegWithPALS-B12
then download the spec files and their contents:
Human.PALS_B12.RIGHT_HEM.with-COLIN-DATA.73730.spec
Human.PALS_B12.LEFT_HEM.with-COLIN-DATA.73730.spec

David VE

On Mar 31, 2009, at 8:22 PM, Jinhui Wang wrote:

> Thank you for your information. I think caret is really a huge  
> project.:-)
>
> 2009/4/1 Donna Dierker <donna at 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
> > 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
> >>> _______________________________________________
> >>> caret-users mailing list
> >>> caret-users at brainvis.wustl.edu
> >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>>
> >> _______________________________________________
> >> caret-users mailing list
> >> caret-users at brainvis.wustl.edu
> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>
> >>
> >>
> >> --
> >> 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
> >> _______________________________________________
> >> caret-users mailing list
> >> caret-users at brainvis.wustl.edu
> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>
> >
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> >
>
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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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