Hi Anna, don't use --projfrac-avg as that will average the values over the ribbon (and so give non-integer results). Just use --projfrac
On 2/4/16 9:07 AM, Gardumi Anna (PSYCHOLOGY) wrote:
Dear all,
I have checked the result of projecting a map from volume to surface with nearest neighbor "interpolation" with 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
and the resulting map does contain additional values which were not present in the original volume map (I used a map with discrete values so that it is easy to check for). Therefore, it seems to me that there should be at some point of the projection pipeline an interpolation/averaging procedure. Could you, please, clarify me where this interpolation/averaging take place when using the option "--interp nearest" or whether I am making a mistake in the command line?
I still hope to be able to average across the cortex depth excluding from such averaging voxels with a specific value (e.g. 0, which would represent voxels for which the map is not defined). Is this possible?
Finally, I would like to automatize taking screenshots of the resulting surface maps. I am using the following script: freeview -f DiscreteMap_SurfLh.mgh:overlay_threshold=-10,10 -cam Azimuth -35 Zoom 1.5 Elevation 5 Roll 0 -ss test How can I set the colormap to "Color Wheel" option "Inverse" (i.e. low to high values = blue to red) via command line?
Thank you in advance for your help! Anna
-----Original Message----- From: Gardumi Anna (PSYCHOLOGY) Sent: maandag 1 februari 2016 17:57 To: 'Freesurfer support list' Subject: RE: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values
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:
- 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);
- averaging of the value obtained from point 1) Is this correct?
What I would like is the following:
- 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])
- 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.
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