Ok, maybe I'm making this question too intricate. Here's the short version:
How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation?
Thanks again, Clark
Hi Freesurfers,
I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only.
My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask
Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data?
Thanks, Clark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation?
Thanks again, Clark
Hi Freesurfers,
I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only.
My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask
Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data?
Thanks, Clark _______________________________________________ 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.
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer). I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ 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.
I'll leave that for Doug. Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer). I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ 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.
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer).
Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps… (then again, I do not know any statistician...)
best Sebastian
I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ 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
Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model.
At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well.
I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own.
-Clark
On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote:
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer).
Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps… (then again, I do not know any statistician...)
best Sebastian
I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ 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
-- Sebastian Moeller
telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Hi Clark,
If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docshttp://nipy.sourceforge.net/nipy/stable/api/generated/nipy.algorithms.statistics.empirical_pvalue.html /sourcehttps://github.com/nipy/nipy/blob/master/nipy/algorithms/statistics/empirical_pvalue.py). I've never used these, but they look pretty straightforward.
Also it looks like FDR is built into mri_surfcluster.
Best, Michael
On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher cfisher@mail.rockefeller.eduwrote:
Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model.
At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well.
I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own.
-Clark
On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote:
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking
for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer).
Does it really correct the map? I thought all it does is figureout the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps… (then again, I do not know any statistician...)
best Sebastian
I recognize that this may not be an officially supported functionality,
but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to
compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short
version:
How can I FDR correct painted surface significance maps when I have
no talraich .xfm file and no cortical segmentation?
Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output
FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however:
1) I don't have any .xfm files for my monkeys, as I'm working innative space, and
2) Without segmentation, I don't have a good mask to use for thecortex only. My first attempts at work-arounds would be:
1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex maskShould these work? If so, how should I make an identity .xfm file?
If not, is there another way to FDR correct my surface data?
Thanks, Clark _______________________________________________ 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
-- Sebastian Moeller
telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Michael, I'll look into Nipy's FDR tools. I actually started this thread asking for help getting mri_surfcluster running for my situation (I have no talraich .xfm and no segmentation for my monkeys). The silence on that topic suggest that it might not be possible, or it's at least not known to possible.
Thanks again everyone.
-Clark
On Aug 29, 2012, at 6:55 PM, Michael Waskom wrote:
Hi Clark,
If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docshttp://nipy.sourceforge.net/nipy/stable/api/generated/nipy.algorithms.statistics.empirical_pvalue.html/sourcehttps://github.com/nipy/nipy/blob/master/nipy/algorithms/statistics/empirical_pvalue.py). I've never used these, but they look pretty straightforward.
Also it looks like FDR is built into mri_surfcluster.
Best, Michael
On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher <cfisher@mail.rockefeller.edumailto:cfisher@mail.rockefeller.edu> wrote: Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model.
At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well.
I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own.
-Clark
On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote:
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer).
Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps… (then again, I do not know any statistician...)best Sebastian
I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Sebastian Moeller
telephone: +1-626-325-8598tel:%2B1-626-325-8598 /+1-626-395-6523tel:%2B1-626-395-6523 / +1-626-395-6616tel:%2B1-626-395-6616 fax: 626-395-8826tel:626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41tel:%2B49%20-%2015%2077%20-%201%2090%2031%2041 mobile: +1-626-325-8598tel:%2B1-626-325-8598 +1-626-807-5242tel:%2B1-626-807-5242 US CDMA: +1-626-807-5242tel:%2B1-626-807-5242 moeller@caltech.edumailto:moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Clark
sorry, the end of the summer has been a period when things slip through the cracks. I think what you want is possible without a talairach or aseg, but it will need to wait for Doug to get back. Can you repost at the end of next week? Bruce
On Thu, 30 Aug 2012, Clark Fisher wrote:
Thanks Michael, I'll look into Nipy's FDR tools. I actually started this thread asking for help getting mri_surfcluster running for my situation (I have no talraich .xfm and no segmentation for my monkeys). The silence on that topic suggest that it might not be possible, or it's at least not known to possible. Thanks again everyone.
-Clark
On Aug 29, 2012, at 6:55 PM, Michael Waskom wrote:
Hi Clark,If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docs/source). I've never used these, but they look pretty straightforward.
Also it looks like FDR is built into mri_surfcluster.
Best, Michael
On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher cfisher@mail.rockefeller.edu wrote: Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model. At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well. I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own. -Clark On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: > Hi Clark, > > > On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: > >> Hi Bruce, >> >> Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer). > > Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps? (then again, I do not know any statistician...) > > > best > Sebastian > >> I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way? >> >> Best, >> Clark >> >> >> On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote: >> >>> Hi Clark >>> >>> you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface. >>> >>> cheers >>> Bruce >>> On Tue, 28 Aug 2012, Clark Fisher wrote: >>> >>>> Ok, maybe I'm making this question too intricate. Here's the short version: >>>> How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? >>>> Thanks again, >>>> Clark >>>> Hi Freesurfers, >>>> I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: >>>> 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and >>>> 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: >>>> 1)Try to create an identity .xfm file >>>> 2)Use the cortical ribbons from mris_volmask as a cortex mask >>>> Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? >>>> Thanks, >>>> Clark >>>> _______________________________________________ >>>> 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 > > -- > Sebastian Moeller > > telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 > fax: 626-395-8826 > German GSM: +49 - 15 77 - 1 90 31 41 > mobile: +1-626-325-8598 > +1-626-807-5242 > US CDMA: +1-626-807-5242 > moeller@caltech.edu > > Division of Biology > MC 114-96 > California Institute of Technology > 1200 East California Boulevard > CA 91125, Pasadena > USA > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Will do. Thanks again.
-Clark
On Sep 3, 2012, at 2:33 PM, Bruce Fischl wrote:
Hi Clark
sorry, the end of the summer has been a period when things slip through the cracks. I think what you want is possible without a talairach or aseg, but it will need to wait for Doug to get back. Can you repost at the end of next week? Bruce
On Thu, 30 Aug 2012, Clark Fisher wrote:
Thanks Michael, I'll look into Nipy's FDR tools. I actually started this thread asking for help getting mri_surfcluster running for my situation (I have no talraich .xfm and no segmentation for my monkeys). The silence on that topic suggest that it might not be possible, or it's at least not known to possible. Thanks again everyone. -Clark On Aug 29, 2012, at 6:55 PM, Michael Waskom wrote:
Hi Clark,If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docs/source). I've never used these, but they look pretty straightforward. Also it looks like FDR is built into mri_surfcluster. Best, Michael On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher cfisher@mail.rockefeller.edu wrote: Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model. At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well. I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own. -Clark On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: > Hi Clark, > > > On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: > >> Hi Bruce, >> >> Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer). > > Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps? (then again, I do not know any statistician...) > > > best > Sebastian > >> I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way? >> >> Best, >> Clark >> >> >> On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote: >> >>> Hi Clark >>> >>> you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface. >>> >>> cheers >>> Bruce >>> On Tue, 28 Aug 2012, Clark Fisher wrote: >>> >>>> Ok, maybe I'm making this question too intricate. Here's the short version: >>>> How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? >>>> Thanks again, >>>> Clark >>>> Hi Freesurfers, >>>> I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: >>>> 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and >>>> 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: >>>> 1)Try to create an identity .xfm file >>>> 2)Use the cortical ribbons from mris_volmask as a cortex mask >>>> Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? >>>> Thanks, >>>> Clark >>>> _______________________________________________ >>>> 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 > > -- > Sebastian Moeller > > telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 > fax: 626-395-8826 > German GSM: +49 - 15 77 - 1 90 31 41 > mobile: +1-626-325-8598 > +1-626-807-5242 > US CDMA: +1-626-807-5242 > moeller@caltech.edu > > Division of Biology > MC 114-96 > California Institute of Technology > 1200 East California Boulevard > CA 91125, Pasadena > USA > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Clark, I just made a modification to mri_binarize to make it take an FDR as input. It computes the threshold and binarizes the input based on the threshold. I've put a copy here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.linux
Run it with --help to get more info.
doug
On 08/29/2012 02:08 PM, Clark Fisher wrote:
Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model.
At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well.
I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own.
-Clark
On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote:
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer).
Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps… (then again, I do not know any statistician...)
best Sebastian
I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ 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
-- Sebastian Moeller
telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
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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Bruce Fischl -
Clark Fisher -
Douglas N Greve -
Michael Waskom -
Sebastian Moeller