Dear FreeSurfer experts:
When I registered the map of functional activation on each hemisphere, how can I extract mean activation value based on each parcellation region on the surface?
According to FreeSurfer tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/IndividualF...
, the measures extracted by mri_segstats is the functional activation map resampled to the individual's anatomical space by mri_vol2vol. Can mri_segstats extract mean activation value based on each parcellation region in a surface-based way?
Thank you for your time!
Best, Foucault
If you want to extract data that is already on the surface, you can use mri_segstats with the --annot option. If you want time courses as the output, use the --avgwf. Also, you'll probably want to add --exclude 0 to not report data from unknown regions.
On 3/16/18 7:23 AM, zuxfoucault Wong wrote:
Dear FreeSurfer experts:
When I registered the map of functional activation on each hemisphere, how can I extract mean activation value based on each parcellation region on the surface?
According to FreeSurfer tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/IndividualF...
, the measures extracted by mri_segstats is the functional activation map resampled to the individual's anatomical space by mri_vol2vol. Can mri_segstats extract mean activation value based on each parcellation region in a surface-based way?
Thank you for your time!
Best, Foucault
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Dr. Greve,
I can get the surface (Area_mm2) mean sig value by the command: mri_segstats \ --annot subid rh aparc\ --i sig-rh.nii \ --exclude 0 \ --sum sig-rh.bb.stats
And I registered the functional activation map on the surface by mri_vol2surf --mov sig.nii.gz \ --srcreg register.dat \ --hemi rh \ --o sig-rh.nii \ --projfrac 0.5
Just to make sure I didn’t miss something!
Thanks again for the advice!
Best, Foucault
On Fri, Mar 16, 2018 at 11:27 PM Douglas Greve dgreve@mgh.harvard.edu wrote:
If you want to extract data that is already on the surface, you can use mri_segstats with the --annot option. If you want time courses as the output, use the --avgwf. Also, you'll probably want to add --exclude 0 to not report data from unknown regions.
On 3/16/18 7:23 AM, zuxfoucault Wong wrote:
Dear FreeSurfer experts:
When I registered the map of functional activation on each hemisphere, how can I extract mean activation value based on each parcellation region on the surface?
According to FreeSurfer tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/IndividualF...
, the measures extracted by mri_segstats is the functional activation map resampled to the individual's anatomical space by mri_vol2vol. Can mri_segstats extract mean activation value based on each parcellation region in a surface-based way?
Thank you for your time!
Best, Foucault
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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.
If you just want the area of the regions, then that will be in the stats/?h.aparc.stats file. The first command will give you mean mean signficance in each parcellation which is going to be hard to interpret. The mri_vol2surf command looks right
On 3/17/18 11:43 AM, zuxfoucault Wong wrote:
Thanks Dr. Greve,
I can get the surface (Area_mm2) mean sig value by the command: mri_segstats \ --annot subid rh aparc\ --i sig-rh.nii \ --exclude 0 \ --sum sig-rh.bb.stats
And I registered the functional activation map on the surface by mri_vol2surf --mov sig.nii.gz \ --srcreg register.dat \ --hemi rh \ --o sig-rh.nii \ --projfrac 0.5
Just to make sure I didn’t miss something!
Thanks again for the advice!
Best, Foucault
On Fri, Mar 16, 2018 at 11:27 PM Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
If you want to extract data that is already on the surface, you can use mri_segstats with the --annot option. If you want time courses as the output, use the --avgwf. Also, you'll probably want to add --exclude 0 to not report data from unknown regions. On 3/16/18 7:23 AM, zuxfoucault Wong wrote:Dear FreeSurfer experts: When I registered the map of functional activation on each hemisphere, how can I extract mean activation value based on each parcellation region on the surface? According to FreeSurfer tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/IndividualFMRI , the measures extracted by mri_segstats is the functional activation map resampled to the individual's anatomical space by mri_vol2vol. Can mri_segstats extract mean activation value based on each parcellation region in a surface-based way? Thank you for your time! Best, Foucault _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
-
Douglas Greve -
zuxfoucault Wong