Hi, FreeSurfers. Is it possible to use FreeSurfer's group analysis tools to investigate surface deformation instead of thickness? I guess it would be interesting for subcortical structures like putamen, amygdala or hippocampus. Let's say you get the putamen data from 15 subjects and compare it to putamen data from fsaverage, After correct registration, I guess we can detect regions of contraction and expansion leading to changes in the putamen contour. I imagined it could be done if we calculate the signed Euclidean distances between the corresponding points of for each subject's putamen and fsaverage, with positive and negative values indicating, for example, the presence of an outward or inward surface deformation. After all calculation I guess we can get a similar result to the pictures we can see at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis but showing only a putamen and the colors meaning surface deformation instead of thickness. This way, you can notice morphological differences among subjects even if they have the same volume. Thanks in advance, Marcos
Hi Marcos, we're not really set up to do this kind of thing. The subcortical structures in fsaverage are not appropriate for surface-based analysis. We do not generate surface for subcortical structures from individuals. I think FSL might do this kind of thing. doug
On 08/07/2013 04:03 PM, Marcos Martins da Silva wrote:
Hi, FreeSurfers. Is it possible to use FreeSurfer's group analysis tools to investigate surface deformation instead of thickness? I guess it would be interesting for subcortical structures like putamen, amygdala or hippocampus. Let's say you get the putamen data from 15 subjects and compare it to putamen data from fsaverage, After correct registration, I guess we can detect regions of contraction and expansion leading to changes in the putamen contour. I imagined it could be done if we calculate the signed Euclidean distances between the corresponding points of for each subject's putamen and fsaverage, with positive and negative values indicating, for example, the presence of an outward or inward surface deformation. After all calculation I guess we can get a similar result to the pictures we can see at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis%A0 but showing only a putamen and the colors meaning surface deformation instead of thickness. This way, you can notice morphological differences among subjects even if they have the same volume. Thanks in advance, Marcos
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for your answer, Doug. Cheers, Marcos Em Qua, 2013-08-07 às 19:32 -0400, Douglas N Greve escreveu:
Hi Marcos, we're not really set up to do this kind of thing. The subcortical structures in fsaverage are not appropriate for surface-based analysis. We do not generate surface for subcortical structures from individuals. I think FSL might do this kind of thing. doug
On 08/07/2013 04:03 PM, Marcos Martins da Silva wrote:
Hi, FreeSurfers. Is it possible to use FreeSurfer's group analysis tools to investigate surface deformation instead of thickness? I guess it would be interesting for subcortical structures like putamen, amygdala or hippocampus. Let's say you get the putamen data from 15 subjects and compare it to putamen data from fsaverage, After correct registration, I guess we can detect regions of contraction and expansion leading to changes in the putamen contour. I imagined it could be done if we calculate the signed Euclidean distances between the corresponding points of for each subject's putamen and fsaverage, with positive and negative values indicating, for example, the presence of an outward or inward surface deformation. After all calculation I guess we can get a similar result to the pictures we can see at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis%A0 but showing only a putamen and the colors meaning surface deformation instead of thickness. This way, you can notice morphological differences among subjects even if they have the same volume. Thanks in advance, Marcos
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Marcos Martins da Silva