[caret-users] Creating a surface-based atlas from a volumetric-atlas
Dear all, I have an averaged T1-image and co-registered volumetric atlas of the macaque brain (which has been digitized by a collaborator) and want to derive from it a surface-based atlas. Subsequently, I would like to use this atlas to get a parcellation of the cortical surface of an individual macaque brain). How should I approach this problem? I have extracted the cortical surface from the averaged T1-weigthed scan. Should I now just label each cortical vertex by determining to which ROI it belongs? And what if some vertices fall outside all ROI's? Also, the result does not look so smooth as existing atlases. And to parcellate an individual macaque brain, can I register both the surfaces (that is, the template surface and the individual surface) spherically? Thanks a lot, Rikkert ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] threshold of metric file
Hi wangzhiwei, I'm a little confused by the question. There mention of area size and scales hints that there might be a confusion between tools used for quantification / significance testing and those used for display purposes. Freesurfer has its own tools for significance testing, so you could use those. We often use threshold-free cluster enhancement for that purpose, which finds the significance threshold. Suprathreshold area can be computed once this threshold has been determined. But usually when I make a figure, I generate border around the suprathreshold regions and display these bordersover the real t- or f-map, using a scale that corresponds to my alpha (e.g., .05) divided by two (since I usually do both right and left hem tests). I compute this t or f-stat using my n / degrees of freedom. So the significance testing and display steps are separate, the way I do it. Now you might not be going as far as significance testing. Sometimes you just want to look at some preliminary data -- particularly for a single subject. A good start might be to understand if this is a single subject, group results, what kind of statistic. And certainly not everyone does this the way I do, so it would be helpful for others to weigh in with their viewpoints/conventions. Donna On Oct 28, 2014, at 9:53 PM, wangzhiwei3233 wangzhiwei3...@126.com wrote: Hi, experts, I converted fMRI results derived from freesurfer to caret, and not I want to count activation areas on caret. So there is a problem of threshold and scale. Auto scale range is 0~60. I found that the area size was different when using scale 1.3~4 from when using scale 1.3~60. And the latter one was smaller. However , in the latter case(1.3~60), the value of a point that was next to the border of activation area but in non-activation area was a little bit lager than the threshold 1.3. How to set the scale to guarantee the activation accurate? Best! ___ 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] threshold of metric file
Hi, Donna, My purpose is counting activated area size on each subject. I did do significance test using Freesurfer on individual level. The results contained many files,for example, sig.nii.gz and Fsig.nii.gz corresponding to result of t and f test respectively. Is that right? But I do not know how to determine tha suprathreshold on subject level as you mentioned. For display and counting area size, I converted the results file(sig.nii.gz) to Caret. Then I count area size on Caret. When I counted area size, I selected a uniform threshold 1.3, i.e.-log10(0.05) for each subject. So I set the scale to 1.3 ~ maxminum on Caret. Is this right? So I could draw a border around the suprathreshold region and generated a paint file. I got the area size of the region using the paint file. Is there any step wrong? Thanks! Zhiwei At 2014-10-30 00:27:14, Donna Dierker do...@brainvis.wustl.edu wrote: Hi wangzhiwei, I'm a little confused by the question. There mention of area size and scales hints that there might be a confusion between tools used for quantification / significance testing and those used for display purposes. Freesurfer has its own tools for significance testing, so you could use those. We often use threshold-free cluster enhancement for that purpose, which finds the significance threshold. Suprathreshold area can be computed once this threshold has been determined. But usually when I make a figure, I generate border around the suprathreshold regions and display these bordersover the real t- or f-map, using a scale that corresponds to my alpha (e.g., .05) divided by two (since I usually do both right and left hem tests). I compute this t or f-stat using my n / degrees of freedom. So the significance testing and display steps are separate, the way I do it. Now you might not be going as far as significance testing. Sometimes you just want to look at some preliminary data -- particularly for a single subject. A good start might be to understand if this is a single subject, group results, what kind of statistic. And certainly not everyone does this the way I do, so it would be helpful for others to weigh in with their viewpoints/conventions. Donna On Oct 28, 2014, at 9:53 PM, wangzhiwei3233 wangzhiwei3...@126.com wrote: Hi, experts, I converted fMRI results derived from freesurfer to caret, and not I want to count activation areas on caret. So there is a problem of threshold and scale. Auto scale range is 0~60. I found that the area size was different when using scale 1.3~4 from when using scale 1.3~60. And the latter one was smaller. However , in the latter case(1.3~60), the value of a point that was next to the border of activation area but in non-activation area was a little bit lager than the threshold 1.3. How to set the scale to guarantee the activation accurate? Best! ___ 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
