[FieldTrip] vtpm atlas contains no right IPS5

Anne Urai anne.urai at gmail.com
Tue Jul 18 10:12:26 CEST 2017

Dear Liang,
cc Tzvetan, FieldTrip

See the conversation below - Tzvetan has indicated that the volumetric
representation is already missing IPS5. It would be great to try and redo
the projection into volume space and play with the threshold to make sure
that all regions are at least assigned to one voxel.


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

From: Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
<tzvetan.popov at uni-konstanz.de>
Reply: FieldTrip discussion list <fieldtrip at science.ru.nl>
<fieldtrip at science.ru.nl>
Date: 18 July 2017 at 09:28:28
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
<fieldtrip at science.ru.nl>
Subject:  Re: [FieldTrip] vtpm atlas contains no right IPS5

Dear Anne,

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

I have created the mat file working from the nifti files. I don’t have the
code anymore but it wasn’t too difficult. Yet, this code wouldn’t help
since the ROI isn’t in the nifti files to begin with. I had exchange RE:
missing ROI with Michael Arcaro back then. Here is what he wrote:

"As you said, ROI 23 does not appear to be in the volume lh map.
It’s there in the surface max prob map for the lh. I know Liang generated a
separate probability map using nonlinear volumetric alignment, which was a
little bit worse in quality than the surface map. It’s possible you’re
using that map. I thought we sent you the volume projection of the surface
max probability map though. It’s possible that the small area of ROI3 in
the surface max probability map did not survive the projection back into
volume space (since there is interpolation in the projection). I’ll double
check with Liang and Ryan and see if they remember any issues with ROI23.
It might be better to use the individual probability map for ROI 23 and use
a more liberal threshold."

So it seems that Liang could indeed provide some more info on whether and
how to use a more liberal threshold to get the ROI back into the volumetric


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