Hi Freesurfers,
I'd like to use mris_make_face_parcellation to downsample an individual subject's surface mesh to a resolution similar to fsaverage6.
My understanding is that mris_make_face_parcellation should let me do this, and it does what I expect with ic3-5. However when I run it with ic6 as the target, it fails:
[surf]$ mris_make_face_parcellation lh.sphere $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot Reading lh.sphere Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri parcellating hemisphere into 40962 units INFO: CTABunique() could not find a unique set in 10 tries INFO: CTABunique() could not find a unique set in 100 tries ERROR: could not find a unique color table
I don't really care if the colors themselves are distinct, and it should be possible to just programmatically generate a valid color table (since 255 ^ 3 > 40962). I thought that providing a colortable with unique values through the -ctab option might work, but looking at the source code it seems that option will *write* a colortable, not read one.
So, is there any way to accomplish the downsampling I want?
Thanks in advance, Michael
Hi Michael,
I think this is a problem that crops up periodically for us in the MEEG world, where we use these downsampling as calculated in MNE. If my memory serves, as you go to higher resolutions you end up with multiple points being mapped to the same location, which I don't believe we have ever found a solution to. Note, this can even happen at ico 5 (particularly on smaller brains).
hth d
On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom mwaskom@stanford.edu wrote:
Hi Freesurfers,
I'd like to use mris_make_face_parcellation to downsample an individual subject's surface mesh to a resolution similar to fsaverage6.
My understanding is that mris_make_face_parcellation should let me do this, and it does what I expect with ic3-5. However when I run it with ic6 as the target, it fails:
[surf]$ mris_make_face_parcellation lh.sphere $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot Reading lh.sphere Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri parcellating hemisphere into 40962 units INFO: CTABunique() could not find a unique set in 10 tries INFO: CTABunique() could not find a unique set in 100 tries ERROR: could not find a unique color table
I don't really care if the colors themselves are distinct, and it should be possible to just programmatically generate a valid color table (since 255 ^ 3 > 40962). I thought that providing a colortable with unique values through the -ctab option might work, but looking at the source code it seems that option will *write* a colortable, not read one.
So, is there any way to accomplish the downsampling I want?
Thanks in advance, Michael
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi,
Can you say a bit more about what you mean?
If my memory serves, as you go to higher resolutions you end up with
multiple points being mapped to the same location,
Do you mean multiple icosahedron vertices being mapped to the same native mesh vertex, or the other way around?
In any case, the issue here is a little bit different, in that it is just raised when trying to generate a color table for the annotation: https://github.com/neurodebian/freesurfer/blob/master/utils/colortab.c#L540
Michael
On Fri, Mar 25, 2016 at 11:27 AM, dgw dgwakeman@gmail.com wrote:
Hi Michael,
I think this is a problem that crops up periodically for us in the MEEG world, where we use these downsampling as calculated in MNE. If my memory serves, as you go to higher resolutions you end up with multiple points being mapped to the same location, which I don't believe we have ever found a solution to. Note, this can even happen at ico 5 (particularly on smaller brains).
hth d
On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom mwaskom@stanford.edu wrote:
Hi Freesurfers,
I'd like to use mris_make_face_parcellation to downsample an individual subject's surface mesh to a resolution similar to fsaverage6.
My understanding is that mris_make_face_parcellation should let me do
this,
and it does what I expect with ic3-5. However when I run it with ic6 as
the
target, it fails:
[surf]$ mris_make_face_parcellation lh.sphere $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot Reading lh.sphere Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri parcellating hemisphere into 40962 units INFO: CTABunique() could not find a unique set in 10 tries INFO: CTABunique() could not find a unique set in 100 tries ERROR: could not find a unique color table
I don't really care if the colors themselves are distinct, and it should
be
possible to just programmatically generate a valid color table (since
255 ^
3 > 40962). I thought that providing a colortable with unique values
through
the -ctab option might work, but looking at the source code it seems that option will *write* a colortable, not read one.
So, is there any way to accomplish the downsampling I want?
Thanks in advance, Michael
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
first caveat, I could be wrong:
On Fri, Mar 25, 2016 at 3:18 PM, Michael Waskom mwaskom@stanford.edu wrote:
Hi,
Can you say a bit more about what you mean?
If my memory serves, as you go to higher resolutions you end up with multiple points being mapped to the same location,
Do you mean multiple icosahedron vertices being mapped to the same native mesh vertex, or the other way around?
I can't remember correctly, this is one of those cases, where I remember it was surprising and confusing, but can't remember what the right answer was
In any case, the issue here is a little bit different, in that it is just raised when trying to generate a color table for the annotation: https://github.com/neurodebian/freesurfer/blob/master/utils/colortab.c#L540
I'm wondering if that is just a quirk of the error reporting, because the check for multiple vertices in FreeSurfer is at the colortab stage.
hth d
Michael
On Fri, Mar 25, 2016 at 11:27 AM, dgw dgwakeman@gmail.com wrote:
Hi Michael,
I think this is a problem that crops up periodically for us in the MEEG world, where we use these downsampling as calculated in MNE. If my memory serves, as you go to higher resolutions you end up with multiple points being mapped to the same location, which I don't believe we have ever found a solution to. Note, this can even happen at ico 5 (particularly on smaller brains).
hth d
On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom mwaskom@stanford.edu wrote:
Hi Freesurfers,
I'd like to use mris_make_face_parcellation to downsample an individual subject's surface mesh to a resolution similar to fsaverage6.
My understanding is that mris_make_face_parcellation should let me do this, and it does what I expect with ic3-5. However when I run it with ic6 as the target, it fails:
[surf]$ mris_make_face_parcellation lh.sphere $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot Reading lh.sphere Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri parcellating hemisphere into 40962 units INFO: CTABunique() could not find a unique set in 10 tries INFO: CTABunique() could not find a unique set in 100 tries ERROR: could not find a unique color table
I don't really care if the colors themselves are distinct, and it should be possible to just programmatically generate a valid color table (since 255 ^ 3 > 40962). I thought that providing a colortable with unique values through the -ctab option might work, but looking at the source code it seems that option will *write* a colortable, not read one.
So, is there any way to accomplish the downsampling I want?
Thanks in advance, Michael
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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
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.
freesurfer@nmr.mgh.harvard.edu
-
dgw -
Michael Waskom