It's very kind of you. Thanks very much. 2009/4/1 David Van Essen <vanes...@brainvis.wustl.edu>
> 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 <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 > _______________________________________________ > 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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