AW: [FIELDTRIP] clarification: coordinates and volumelookup

[Jan Hirschmann]

Thanks Ingrid,

 

your comments were of much help to me. I did not know that one can plot
the atlas and about the function of cfg.maxqueryrange. So it means sth
like: search in the x closest voxels for labels? 

 

 The warning occurs in read_mri at line 105. There it says:

 

% FIXME: this should be checked, but I only have a single BRIK file

% construct the homogenous transformation matrix that defines the axes

 warning('homogenous transformation might be incorrect for AFNI file');

 

Thanks very much for your help!

 

Jan

 

________________________________

Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im
Auftrag von Ingrid Nieuwenhuis
Gesendet: Freitag, 4. Juni 2010 16:47
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: Re: [FIELDTRIP] clarification: coordinates and volumelookup

 

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.

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20100607/7f10941a/attachment-0001.html>