[FieldTrip] vtpm atlas contains no right IPS5

[Anne Urai]

Hi Tvetan,
Thanks for your help.

Dear Anne,>* The description on
http://www.fieldtriptoolbox.org/template/atlas
<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
<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?
*this information was provided by the principle investigator of the
paper. You might ask the corresponding author for further details on
this.
Best
tzvetan

I've been in touch with Dr. Liang Wang (first author on the paper), but he
could only point me to the original NIfTI files on the website which have
been converted in AFNI. Do you know by any chance which author provided the
mat file, so I can work from the code they used?

Best,

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

From: Anne Urai <anne.urai at gmail.com> <anne.urai at gmail.com>
Reply: Anne Urai <anne.urai at gmail.com> <anne.urai at gmail.com>
Date: 10 July 2017 at 10:38:59
To: fieldtrip at science.ru.nl <fieldtrip at science.ru.nl>
<fieldtrip at science.ru.nl>
Subject:  vtpm atlas contains no right IPS5

Dear Fieldtrippers,

I'm using the VTPM atlas to define masks for all the visual regions
described in the paper (Wang et al. 2014,
https://academic.oup.com/cercor/article-lookup/doi/10.1093/cercor/bhu277).
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?

Thanks!

—
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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