Dear Donna and David, Thanks for your kind suggests. Using hemi-specific PALS-B12, here I can observe the completely consistent results from CARET and MRIcron. Functional results mapped onto surface are really nice. Alao, following CARET guideline, I just selected AFM rather than MFM, which indeed produced different results. Empolyed mapping algorithm was mapping enclosing voxel.
Thanks again, Liang 2009/5/27 David Van Essen <vanes...@brainvis.wustl.edu> > Dr. Wang, > > Donna's suggestions are good ones. Two other possibilities spring to > mind. > > 1) Are you looking at the results of multi-fiducial mapping (chosen in > the 'mapping atlas' window once you have selected the PALS_B12 atlas > left or right hemiephere)? This gives substantially different results > than 'average fiducial mapping', for reasons explained in Van Essen > (Neuroimage 2005). > > 2) Did you choose a non-standard mapping in the 'mapping algorithm' > window? (e.g., a METRIC_AVERAGE_VOXEL with a large Neighbor box size > that would blur the results) > > If none of these suggestions work out, it may be useful to upload the > data so that Donna can look more closely at what's going on. > > David VE > > On May 27, 2009, at 8:07 AM, Donna Dierker wrote: > > > Hi Dr. Wang, > > > > Are you by any chance using a BOTH spec file to display your results? > > When sorting out problems like this, I find it is helpful to use > > hemisphere-specific spec files. For example, the > > CARET_TUTORIAL_SEPT06 > > has these three spec files: > > > > PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec > > PALS_B12.LEFT.STANDARD-SCENES.73730.spec > > PALS_B12.RIGHT.STANDARD-SCENES.73730.spec > > > > If you are using PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec, then > > using PALS_B12.LEFT.STANDARD-SCENES.73730.spec and > > PALS_B12.RIGHT.STANDARD-SCENES.73730.spec independently, to see if > > your > > problem persists. I suspect it might be mapping okay, but you are > > displaying the left hem result on the right hem, or vice versa. > > Getting > > only one hem in your Caret session will help us rule out such > > problems. > > > > The only other explanation I can come up with is unlikely. If your > > volumes were Analyze, rather than NIfTI, then it might be possible to > > open the .hdr for one hem and specify a flip, but then open it for the > > other hemisphere and not specify a flip. But I thought SPM5 wrote > > NIfTI. (You might be able to specify Analyze, though.) Chances are, > > though, you didn't open your volume through the File: Open Data File: > > Volume Functional file dialog anyway, which is the only way you are > > prompted for a flip. If you load through the mapping wizard, it > > simply > > doesn't flip. > > > > Let's start with the single hem specs and see where that gets us. > > > > Donna > > > > On 05/26/2009 11:57 PM, liang wang wrote: > >> Hi CARET experts, > >> > >> Following the guideline, I successfully used CARET (v5.6.1) to map a > >> functional volume (SPM5 results) to PALS_B12*.spec. However, we found > >> that the displayed results differed from that from MRIcron or SPM5 in > >> the same threshold. Moreover, the results from CARET seemly were > >> symmetric across two hemisphere. Actual results were far away from > >> this situation. I attempted to adjust the threshold in the section > >> "Page selection - Metric setting" to see whether the results from > >> different software could match well. Unfortunately, it did not work > >> well. If you share a solution, I would be appreciated. > >> > >> Thanks in advance, > >> > >> Liang > >> > >> > >> -- > >> Liang Wang, PhD > >> Postdoctoral Fellow > >> Woodward Lab > >> Department of Psychiatry > >> University of British Columbia > >> BC Mental Health & Addiction Services > >> 938 West 28th Avenue > >> Vancouver BC V5Z 4H4 > >> Telephone: 1-604-875-2000 (ext. 4735) > >> Fax: 1-604-875-3871 > >> Email: wangl...@gmail.com <mailto:wangl...@gmail.com> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> 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 > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com
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