[FieldTrip] vtpm atlas contains no right IPS5

[Anne Urai]

Hi Tzvetan, Fieldtrippers,

see below the response I got from Liang Wang.

*I double-check the original files of the maximum probabilistic atlas in
the volume-based space. As you said, it did not include left IPS5 areas. In
our paper, we had pointed out that there was a difference between volume-
and surface-based atlas, because the registration used between two space
was totally different. We think the surface-based atlas may be more
accurate, compare to the volume-based atlas. If you need to get left IPS5,
I suggest to use the probability map for that region that you also can
download from the web. This map provides you a probability value for each
voxel being to that region. *

*Best,*
*Liang*

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

On 18 July 2017 at 10:12, Anne Urai <anne.urai at gmail.com> wrote:

> 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.
>
> 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: 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
> representation?
>
> Best
> tzvetan
>
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