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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Jan,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><span style='mso-list:Ignore'>3)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>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).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hope this helps,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Ingrid<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=NL
style='font-size:10.0pt;font-family:Arial;color:navy'>------------------------------------</span></font><font
color=navy><span lang=NL style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=NL
style='font-size:10.0pt;font-family:Arial;color:navy'>Ingrid
L.C. Nieuwenhuis</span></font><font color=navy><span lang=NL
style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=NL
style='font-size:10.0pt;font-family:Arial;color:navy'>PhD student</span></font><font
color=navy><span lang=NL style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Donders Institute for Brain, Cognition and
Behaviour,</span></font><font color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Centre for Cognitive Neuroimaging</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><U1:PLACENAME u2:st="on"><st1:PlaceName w:st="on"><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Radboud</span></font></st1:PlaceName></U1:PLACENAME><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> <U1:PLACETYPE u2:st="on"><st1:PlaceType w:st="on">University</U1:PLACETYPE></st1:PlaceType>
<U1:CITY u2:st="on"><st1:City w:st="on">Nijmegen</U1:CITY></st1:City>, The <U1:COUNTRY-REGION u2:st="on"><U1:PLACE u2:st="on"><st1:place
w:st="on"><st1:country-region w:st="on">Netherlands</U1:PLACE></U1:COUNTRY-REGION></st1:country-region></st1:place></span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Email: ingrid.nieuwenhuis@donders.ru.nl</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Tel: 0031 (0)24 - 36 10887</span></font><o:p></o:p></p>
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face="Times New Roman"><span style='font-size:12.0pt'>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> <st1:PersonName
w:st="on">FieldTrip discussion list</st1:PersonName>
[mailto:FIELDTRIP@NIC.SURFNET.NL] <b><span style='font-weight:bold'>On Behalf
Of </span></b>Jan Hirschmann<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, June 04, 2010 3:29
PM<br>
<b><span style='font-weight:bold'>To:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style='font-weight:bold'>Subject:</span></b> [FIELDTRIP]
clarification: coordinates and volumelookup</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Best,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Jan<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span lang=DE style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span lang=DE style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>Von:</span></font></b><font size=2
face=Tahoma><span lang=DE style='font-size:10.0pt;font-family:Tahoma'> <st1:PersonName
w:st="on">FieldTrip discussion list</st1:PersonName> [mailto:<st1:PersonName
w:st="on">FIELDTRIP@NIC.SURFNET.NL</st1:PersonName>] <b><span style='font-weight:
bold'>Im Auftrag von </span></b>Jan Hirschmann<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Freitag, 4. Juni 2010
15:21<br>
<b><span style='font-weight:bold'>An:</span></b> <st1:PersonName w:st="on">FIELDTRIP@NIC.SURFNET.NL</st1:PersonName><br>
<b><span style='font-weight:bold'>Betreff:</span></b> [FIELDTRIP] coordinates
and volumelookup</span></font><span lang=DE><o:p></o:p></span></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=DE
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=DE style='font-size:10.0pt;
font-family:Arial'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=DE style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>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:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>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?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>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?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>3)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Thanks for your help!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'>Jan<o:p></o:p></span></font></p>
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<p>----------------------------------</p>
<p>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.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>
<p>----------------------------------</p>
<p>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.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>
<p>----------------------------------</p>
<p>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.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>