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Hi all,<br>
<br>
Let's say you have done some MVPA and want to share your results
with other researchers in terms of areas... why not give them a
NIFTI? Maybe they do not use FSLview or they even co-registered to
another common space, or simply do not like NIFTI ... not nice. So
the only way is to refer to some atlas in order to make sure you are
referring to the very same brain part.<br>
The other way around, maybe they have found something interesting in
a certain area with standard methods and also want a MVPA result,
but do not give you ready to use masks in MNI-space, but just names
of small brain areas. Again an atlas has to be consulted to launch
your MVPA analysis straight away on that area of interest. <br>
So one (not very comfortable way to do this) is to open FSL load the
underlying atlas check the value of your area and have a look at the
xml file to get the right name of that region. In the other case you
start by the xml, open FSL, maybe create a mask which only contains
the area with your value of interest and afterwards you even
co-register it to your subject space... <br>
<br>
The other day I came across the PyMVPA atlas module (which
unfortunately is not yet documented). Looks like that could
definitely simplify life in this kind of case. For example once you
have loaded an atlas, there is the function <tt class="descname">label_voxel</tt><em></em>
which does all the looking up for you:<br>
<br>
>atlas = Atlas(filename="HarvardOxford-Cortical", resolution=2.0)<br>
>atlas.label_voxel([26,26,26],0)<br>
>{'labels': [[{'index': 39, 'label': 'Occipital Fusiform Gyrus',
'prob': 19},<br>
{'index': 22, 'label': 'Lateral Occipital Cortex, inferior
division', 'prob': 12}]],<br>
'voxel_queried': [26, 26, 26]}<br>
<br>
'0.6.0~rc1' even seems to support using a standard FSL xml file for
the atlas (filename) and a custom image file in your subject space
(image_file).<br>
<br>
So is anybody of you already using the atlas module a lot and can
give me a hand with the following example:<br>
- To label: searchlight results in subject space, lets call that
dataset sl_map<br>
- Preferably using Talairach (not my choice) from FSL<br>
- the coordinate system of the atlas modul [26,26,26] would
correspond to the sl_map.fa.voxel_indices!?<br>
- what exactly does this levels option do?<br>
- the other way round should be possible using the find option!? I
tried searching for "Cortex", but as soon as there are multiple
matches the option finishes in an error...<br>
<br>
Any suggestions welcome! Thanks for all the work you did recently!
Those multiple sa options are just great. Super comfortable for our
kind of experiments!<br>
<br>
LG<br>
<br>
Susanne<br>
<pre class="moz-signature" cols="72">--
Susanne Greiner, Dipl.-Phys. Univ.
ICT - Information and Communication Technolgy
International Doctoral School
NeuroInformatics Laboratory (NILab)
Via delle Regole 101, 38100 Mattarello (TN), ITALY
<a class="moz-txt-link-abbreviated" href="mailto:susanne.greiner@unitn.it">susanne.greiner@unitn.it</a> | Phone +39 0361 882762 | Skype cattt84</pre>
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