Hello list,
is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward).
Thanks a lot in advance,
Nicola
PS apologies for the repost - my subject line was incorrect the first time around.
Hi Nicola
I think this gets done in the MEG analysis stream, but perhaps Matti (ccd) can comment. cheers BruceOn Thu, 24 Jan 2013, Nicola Toschi wrote:
Hello list,
is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward).
Thanks a lot in advance,
Nicola
PS apologies for the repost - my subject line was incorrect the first time around.
hi,
what we do with MEG in the MNE package is indeed store downsampled overlays (that actually have a temporal dimension). More specifically we store the values e.g. only at the vertices of the ico5 subdivision and store the ico 5 vertex indices and overlay values. Then to display them on the high resolution freesurfer surface we basically use a smoothing/diffusion process to fill the missing values. For this downsampling to be valid you'll need to make sure the data are smooth enough in order to avoid aliasing.
let me know if you need more details
hope this helps,
Alex
On Thu, Jan 24, 2013 at 3:47 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Nicola
I think this gets done in the MEG analysis stream, but perhaps Matti (ccd) can comment. cheers BruceOn Thu, 24 Jan 2013, Nicola Toschi wrote:
Hello list,
is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward).
Thanks a lot in advance,
Nicola
PS apologies for the repost - my subject line was incorrect the first time around.
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Hi Alex and Bruce,
thanks a lot for your help. Will play around with MNE - looks like it does what I am looking for.
Nicola
On 01/24/2013 07:54 AM, Alexandre Gramfort wrote:
hi,
what we do with MEG in the MNE package is indeed store downsampled overlays (that actually have a temporal dimension). More specifically we store the values e.g. only at the vertices of the ico5 subdivision and store the ico 5 vertex indices and overlay values. Then to display them on the high resolution freesurfer surface we basically use a smoothing/diffusion process to fill the missing values. For this downsampling to be valid you'll need to make sure the data are smooth enough in order to avoid aliasing.
let me know if you need more details
hope this helps,
Alex
On Thu, Jan 24, 2013 at 3:47 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Nicola
I think this gets done in the MEG analysis stream, but perhaps Matti (ccd) can comment. cheers BruceOn Thu, 24 Jan 2013, Nicola Toschi wrote:
Hello list,
is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward).
Thanks a lot in advance,
Nicola
PS apologies for the repost - my subject line was incorrect the first time around.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
If you specifically want to project overlays onto 'mris_decimate'd surfaces, you won't be able to do that. You could, however, generate new overlays using the decimated surface, if that's helpful, using 'mris_curvature_stats' and feeding it the newly downsampled/demicated surface as input.
FWIW.
Best -=R
On 1/23/13 18:07 , Nicola Toschi wrote:
Hello list,
is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward).
Thanks a lot in advance,
Nicola
PS apologies for the repost - my subject line was incorrect the first time around.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Rudolph,
what I would like to have as an end product is a list of overlay values at each vertex of the decimated surface (i.e. I don't want to synthesize anything into ROIs).
The overlays are all freesurfer-specific (curvature, thickness, LGI, etc). I cannot recompute these on the new (decimated) surface, as they will be significantly different and less accurate (they are specific to the geometry of the original surface). Rather, I was looking to downsample highres overlays after smoothing.
So i am not sure your suggestion would work - please let me know if I misunderstood something.
Thanks again for your reprly,
Nicola
On 01/24/2013 04:01 PM, Rudolph Pienaar wrote:
If you specifically want to project overlays onto 'mris_decimate'd surfaces, you won't be able to do that. You could, however, generate new overlays using the decimated surface, if that's helpful, using 'mris_curvature_stats' and feeding it the newly downsampled/demicated surface as input.
FWIW.
Best -=R
On 1/23/13 18:07 , Nicola Toschi wrote:
Hello list,
is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward).
Thanks a lot in advance,
Nicola
PS apologies for the repost - my subject line was incorrect the first time around.
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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Alexandre Gramfort -
Bruce Fischl -
Nicola Toschi -
Rudolph Pienaar