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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 greve@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.