clarification: coordinates and volumelookup

[Ingrid Nieuwenhuis]

Dear Jan,



1)       Yes, I think so. The template is in MNI coordinates. The *10 is
necessary to go from cm to mm. I'm not totally sure if this step is still
necessary, there is some improved handling of units. But it should be easy
to spot if thing are a factor of 10 off.

2)       Depends on the atlas. Some atlases have indeed many voxels (all
white matter for instance) with no label. You can increase
cfg.maxqueryrange, to find the closest label.

3)       Where does the warning come from (file, line?). It sounds indeed if
it's okay, but it's hard to judge without knowing which check in the code
resulted in the warning. Do make sure that the cfg.inputcoordinates set to
'mni' and cfg.atlascoordinates is set to 'tal' (I think the last happens
automatically in ft_prepare_atlas when you use the AFNI file).



What helps to get a bit of insight is to prepare the atlas yourself with
ft_prepare_atlas. You can subsequently plot atlas.brick0 or atlas.brick1
with ft_sourceplot, cfg.funparameter = 'brick0', cfg.interactive = 'yes',
cfg.method = 'orthoplot'. The value is linked to the name in atlas.descr.



Hope this helps,

Ingrid

------------------------------------

Ingrid L.C. Nieuwenhuis

PhD student

Donders Institute for Brain, Cognition and Behaviour,

Centre for Cognitive Neuroimaging

Radboud University Nijmegen, The Netherlands

Email: ingrid.nieuwenhuis at donders.ru.nl

Tel: 0031 (0)24 - 36 10887

  _____

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Jan Hirschmann
Sent: Friday, June 04, 2010 3:29 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] clarification: coordinates and volumelookup



Sorry, 1 thing to clarify in the last question: By "labelling structures I
recognize works fine" I meant setting power to 1 erverywhere and then
defining a roi, e.g. 'Thalamus' in ft_sourceplot. What I see highlighted is
the thalamus.



Best,

Jan



  _____

Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag
von Jan Hirschmann
Gesendet: Freitag, 4. Juni 2010 15:21
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] coordinates and volumelookup



Dear all,



I am using the function ft_volumelookup with the AFNI atlas to find out the
areas belonging to certain MNI coordinates. Regarding this I have 3 little
questions:



1)       If I create a grid from template brain T1 (spm2) and multiply the
.pos entries by 10 to convert to mm, as described in the example matlab
scripts on the fieldtrip homepage, the .pos entries are MNI coordinates,
right?



2)       When I use volumelookup to look up coordinates (I am giving a mask
as input which really has only 1 nonzero entry) I often get the result: "no
label found". Are there really that many places in the brain which do not
have a label in the atlas?



3)       When using the function I get the warning: "homogenous
transformation might be incorrect for AFNI file". Should I worry about this?
Labelling structures I recognize with the tool, e.g. thalamus, works fine,
so I guess labels and cords match.



Thanks for your help!



Jan

----------------------------------

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/

----------------------------------

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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