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<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks Ingrid,<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>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? <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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'> The warning occurs
in read_mri at line 105. There it says:<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>% FIXME: this should be
checked, but I only have a single BRIK file<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'>% construct the
homogenous transformation matrix that defines the axes<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'> warning('homogenous
transformation might be incorrect for AFNI file');<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks very much for your
help!<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>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>
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<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>Von:</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'>Im Auftrag
von </span></b>Ingrid Nieuwenhuis<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Freitag, 4. Juni 2010
16:47<br>
<b><span style='font-weight:bold'>An:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style='font-weight:bold'>Betreff:</span></b> Re: [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 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=2 color=navy face=Arial><span lang=EN-US 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 lang=EN-US 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:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=2 color=navy face=Arial><span lang=EN-US 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 lang=EN-US 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:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=2 color=navy face=Arial><span lang=EN-US 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 lang=EN-US 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 lang=EN-US
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 lang=EN-US
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 lang=EN-US
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 lang=EN-US
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 lang=EN-US
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 lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>Donders Institute for
Brain, Cognition and Behaviour,</span></font><font color=navy><span lang=EN-US
style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>Centre for Cognitive
Neuroimaging</span></font><font color=navy><span lang=EN-US 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 lang=EN-US 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 lang=EN-US 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 lang=EN-US style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>Email:
ingrid.nieuwenhuis@donders.ru.nl</span></font><font color=navy><span
lang=EN-US style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>Tel: 0031 (0)24 - 36
10887</span></font><span lang=EN-US><o:p></o:p></span></p>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span lang=EN-US 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=EN-US
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span lang=EN-US 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><span lang=EN-US><o:p></o:p></span></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-US
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 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 style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>Von:</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:<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><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 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 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:36.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo4'><![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:36.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo4'><![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:36.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo4'><![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>
</div>
</body>
</html>
<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>
<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>