Dear Freesurfers,
Has anyone accomplished analysis of longitudinal cortex changes in a dataset with "flipped" hemispheres?
I am currently struggling with data from stroke patients, half of them with lesions on the right, half of them on the left side of the brain.
What I am planning: flip all healthy hemispheres to left and perform longitud. analysis of cortical thickness change on that (helthy) hemisphere.
I have read the notes on Surface-based Interhemispheric Registration (xhemi) and most of the comments here. It seems to me that this would allow me to compare both hemisph. sides at ONE timepoint. (but not actually analyzing ONE (flipped) hemisphere over time).
Any help to point me in the right direction is greatly appreciated!
Bastian
Hi Bastian,
yes, I have some code to do what you want. You would duplicate and flip the good hemisphere in the image and then run FS on the symmetric heads. This can be done via robust_register and (mis)-using the mid space. You can find some description of this procedure here: *Robust and Accurate Contralateral Registration for Pose Normalization and Tumor Segmentation*. M.Reuter, H.D.Rosas, B.Fischl. /Human Brain Mapping 2012, Beijing http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3458./ http://reuter.mit.edu/blue/papers/reuter-hbm12-tumor/reuter-hbm12-tumor.pdf
and the mid-space registration is described here: *Highly Accurate Inverse Consistent Registration: A Robust Approach*. M. Reuter, H.D. Rosas, B. Fischl. /NeuroImage 53(4):1181-1196, 2010/. http://reuter.mit.edu/papers/reuter-robreg10.pdf
I currently cannot access the folder with the scripts, please send me an email directly ( mreuter@nmr.mgh.harvard.edu ) and I'll send it over as soon as I have access again.
Best, Martin
On 08/12/2014 02:56 AM, Bastian Cheng wrote:
Dear Freesurfers,
Has anyone accomplished analysis of longitudinal cortex changes in a dataset with "flipped" hemispheres?
I am currently struggling with data from stroke patients, half of them with lesions on the right, half of them on the left side of the brain.
What I am planning: flip all healthy hemispheres to left and perform longitud. analysis of cortical thickness change on that (helthy) hemisphere.
I have read the notes on Surface-based Interhemispheric Registration (xhemi) and most of the comments here. It seems to me that this would allow me to compare both hemisph. sides at ONE timepoint. (but not actually analyzing ONE (flipped) hemisphere over time).
Any help to point me in the right direction is greatly appreciated!
Bastian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bastian,
this is in cases where you need to make the images symmetric so that recon-all processing works, but then do the analysis on the original (non flipped) hemisphere in each subject. You should not use this to do a point wise comparison between left (original healthy) and flipped (right originally healthy) hemispheres, as you may introduce a bias. Freesurfer atlases are hemisphere specific.
Best, Martin
On 08/19/2014 01:51 PM, Martin Reuter wrote:
Hi Bastian,
yes, I have some code to do what you want. You would duplicate and flip the good hemisphere in the image and then run FS on the symmetric heads. This can be done via robust_register and (mis)-using the mid space. You can find some description of this procedure here: *Robust and Accurate Contralateral Registration for Pose Normalization and Tumor Segmentation*. M.Reuter, H.D.Rosas, B.Fischl. /Human Brain Mapping 2012, Beijing http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3458./ http://reuter.mit.edu/blue/papers/reuter-hbm12-tumor/reuter-hbm12-tumor.pdf
and the mid-space registration is described here: *Highly Accurate Inverse Consistent Registration: A Robust Approach*. M. Reuter, H.D. Rosas, B. Fischl. /NeuroImage 53(4):1181-1196, 2010/. http://reuter.mit.edu/papers/reuter-robreg10.pdf
I currently cannot access the folder with the scripts, please send me an email directly ( mreuter@nmr.mgh.harvard.edu ) and I'll send it over as soon as I have access again.
Best, Martin
On 08/12/2014 02:56 AM, Bastian Cheng wrote:
Dear Freesurfers,
Has anyone accomplished analysis of longitudinal cortex changes in a dataset with "flipped" hemispheres?
I am currently struggling with data from stroke patients, half of them with lesions on the right, half of them on the left side of the brain.
What I am planning: flip all healthy hemispheres to left and perform longitud. analysis of cortical thickness change on that (helthy) hemisphere.
I have read the notes on Surface-based Interhemispheric Registration (xhemi) and most of the comments here. It seems to me that this would allow me to compare both hemisph. sides at ONE timepoint. (but not actually analyzing ONE (flipped) hemisphere over time).
Any help to point me in the right direction is greatly appreciated!
Bastian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bastian, you can use the interhemispheric analysis to do this study. See https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
A few months ago, someone was trying to do the same thing (or was it you?). In any event, there should be some info in our mail archives doug
On 8/19/14 2:48 PM, Martin Reuter wrote:
Hi Bastian,
this is in cases where you need to make the images symmetric so that recon-all processing works, but then do the analysis on the original (non flipped) hemisphere in each subject. You should not use this to do a point wise comparison between left (original healthy) and flipped (right originally healthy) hemispheres, as you may introduce a bias. Freesurfer atlases are hemisphere specific.
Best, Martin
On 08/19/2014 01:51 PM, Martin Reuter wrote:
Hi Bastian,
yes, I have some code to do what you want. You would duplicate and flip the good hemisphere in the image and then run FS on the symmetric heads. This can be done via robust_register and (mis)-using the mid space. You can find some description of this procedure here: *Robust and Accurate Contralateral Registration for Pose Normalization and Tumor Segmentation*. M.Reuter, H.D.Rosas, B.Fischl. /Human Brain Mapping 2012, Beijing http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3458./ http://reuter.mit.edu/blue/papers/reuter-hbm12-tumor/reuter-hbm12-tumor.pdf
and the mid-space registration is described here: *Highly Accurate Inverse Consistent Registration: A Robust Approach*. M. Reuter, H.D. Rosas, B. Fischl. /NeuroImage 53(4):1181-1196, 2010/. http://reuter.mit.edu/papers/reuter-robreg10.pdf
I currently cannot access the folder with the scripts, please send me an email directly ( mreuter@nmr.mgh.harvard.edu ) and I'll send it over as soon as I have access again.
Best, Martin
On 08/12/2014 02:56 AM, Bastian Cheng wrote:
Dear Freesurfers,
Has anyone accomplished analysis of longitudinal cortex changes in a dataset with "flipped" hemispheres?
I am currently struggling with data from stroke patients, half of them with lesions on the right, half of them on the left side of the brain.
What I am planning: flip all healthy hemispheres to left and perform longitud. analysis of cortical thickness change on that (helthy) hemisphere.
I have read the notes on Surface-based Interhemispheric Registration (xhemi) and most of the comments here. It seems to me that this would allow me to compare both hemisph. sides at ONE timepoint. (but not actually analyzing ONE (flipped) hemisphere over time).
Any help to point me in the right direction is greatly appreciated!
Bastian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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Bastian Cheng -
Douglas Greve -
Martin Reuter