Re: [caret-users] A question when mapping a functional volume to brain surface
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 ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] A question when mapping a functional volume to brain surface
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
Re: [caret-users] A question when mapping a functional volume to brain surface
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
[caret-users] A question when mapping a functional volume to brain surface
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 ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
