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 > >>> > >> _______________________________________________ > >> caret-users mailing list > >> caret-users@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: wjh...@gmail.com > >> wjh122...@yahoo.com.cn > >> _______________________________________________ > >> caret-users mailing list > >> caret-users@brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@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: wjh...@gmail.com wjh122...@yahoo.com.cn
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