[FieldTrip] vtpm atlas contains no right IPS5

Anne Urai anne.urai at gmail.com
Mon Jul 10 10:38:59 CEST 2017

Dear Fieldtrippers,

I'm using the VTPM atlas to define masks for all the visual regions
described in the paper (Wang et al. 2014,
However, there seem to be no entries corresponding to the left IPS5.

*% load atlas*
*atl = ft_read_atlas('~/Documents/fieldtrip/vtpm/vtpm.mat');*
*atl = ft_convert_units(atl, 'cm');*

*% add mni coordinates*
*[ax, ay, az] = voxelcoords(atl.dim, atl.transform);*
*atl.pos = [ax(:) ay(:) az(:)];*

*% make a binary mask for this ROI*
*roi_idx     = find(strcmp(lower(atl.tissuelabel), 'IPS5'));*
*roi_mask = ismember(atl.tissue, roi_idx);*

*% mask the voxels on the right side of the brain*
*rightidx = find(atl.pos(:, 1) > 0); *
*roi_mask(rightidx) = 0;*

Now, sum(roi_mask(:)) = 0. This procedure of separating out the left and
right regions works fine for all other regions in the atlas, as well as the
right IPS5.

The description on http://www.fieldtriptoolbox.org/template/atlas says "The
version of the atlas included with FieldTrip was created by transforming
data into standardized space using surface-based anatomical registration
approaches." Is there any information available on the exact code that was
used to go from this original file
http://scholar.princeton.edu/napl/resources to the mat-file in FieldTrip,
so that I can check where in the process the left IPS5 gets lost?


Anne E. Urai, MSc
PhD student | Institut für Neurophysiologie und Pathophysiologie
Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 |
Hamburg, Germany
www.anneurai.net / @AnneEUrai
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