Thank you for your reply. I am then a bit confused because I thought each surface value was the result of a two-step procedure: 1) sampling of the values along the normal to the surface at the points specified by the option --projfrac-avg min max del; with such values computed according the chosen interpolation method (nearest by default or specified by --interp nearest/trilinear); 2) averaging of the value obtained from point 1) Is this correct?
What I would like is the following: 1) sampling along the normal at the nearest voxel to each point defined by --projfrac-avg min max del (I will obtain for example five values, let's say [1 0 1 2 2]) 2) averaging these values excluding from the mean points having a specific value (e.g. 0 so that I would obtain as a mean value 1.5, and not 1.2) I hope this clarify my point. -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: maandag 1 februari 2016 17:14 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values By default, the projection is done using nearest neighbor "interpolation", so there is no averaging. Is this what you mean? On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote: > > Dear FreeSurfer expert, > > I would like to project my maps from the "original" functional space > (2.5mm iso, same format as COPE images from FSL) to inflated > FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all > pipeline) excluding voxels with a specific value (e.g. 0) from the > averaging procedure of the projection. The reason for this is that I > have non-continuous maps (i.e. map values are defined only for some > voxels; voxels for which map value is not defined will have 0 as > value). Is there a way to perform the projection excluding voxels with > a specific value from the averaging of the projection? > > Thank you in advance for any help! > > Anna > > As complementary information: > > My maps have discrete values (between -10 and 10) and at the moment I > am using the following command: > > mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh > --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap > _InFS_projAvg02_SurfLh.mgh > > However, in this way the resulting surface map will have values biased > by including in the average also the 0 values which in reality > represents voxels not included in the map. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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
