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Hi Jan-Mathijs,<br>
<br>
Thanks for the suggestion.<br>
I tried again with another data set and specified the stat.pos =
grid.pos; stat.inside = grid.inside etc.<br>
And I still get the same issue... the anatomy is not added even when
ft_sourceinterpolate was called.<br>
I can get the stats plotted (weirdly) e.g. screenshot (I hope it
gets through the mail) without the brain anatomy.<br>
<br>
I am not sure what I might be doing wrongly.<br>
<br>
Best,<br>
May<br>
<br>
<br>
<blockquote type="cite"><img
src="cid:part1.09050909.08050701@glasgow.ac.uk" alt=""></blockquote>
<br>
<br>
<div class="moz-cite-prefix">On 09/05/2015 11:00,
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a> wrote:<br>
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<div class="headerdisplayname" style="display:inline;">Subject:
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Re: [FieldTrip] Issues with ft_sourceinterpolate --
missing anatomy</td>
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<div class="headerdisplayname" style="display:inline;">From:
</div>
"Schoffelen, J.M. (Jan Mathijs)"
<a class="moz-txt-link-rfc2396E" href="mailto:jan.schoffelen@donders.ru.nl"><jan.schoffelen@donders.ru.nl></a></td>
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<div class="headerdisplayname" style="display:inline;">Date:
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08/05/2015 12:38</td>
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May,
<div><br>
</div>
<div>Have you ensured that the stat.pos field contains the
dipole positions, coregistered to the template brain?</div>
<div><br>
</div>
<div>Best,</div>
<div>Jan-Mathijs</div>
<div><br>
<div>
<div>On May 8, 2015, at 1:22 PM, Heng-Ru May Tan <<a
moz-do-not-send="true"
href="mailto:Heng-RuMay.Tan@glasgow.ac.uk">Heng-RuMay.Tan@glasgow.ac.uk</a>>
wrote:</div>
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<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#333300">Hi Fieldtrippers<br>
<br>
[The previous email didn't display properly so resending
this again.]<br>
<br>
I am having trouble running ft_sourceinterpolate... I
didn't seem to have this issue before. =(<br>
The anatomy seems to be missing and so when I
subsequently call ft_sourceplot, the brain anatomy is
not 'available' for plotting.<br>
Here are some example of the things I tried and the
errors in hope that someone might be able help!<br>
<br>
Many thanks in advance,<br>
May<br>
<br>
-- this is a stat structure used:<br>
<br>
stat =<br>
prob: [33480x1 double]<br>
cirange: [33480x1 double]<br>
mask: [33480x1 logical]<br>
stat: [33480x1 double]<br>
ref: [33480x1 double]<br>
df: 185<br>
critval: [-1.9729 1.9729]<br>
dim: [33480 1]<br>
inside: [10354x1 double]<br>
outside: [23126x1 double]<br>
pos: [33480x3 double]<br>
freq: 64.9309<br>
cfg: [1x1 struct]<br>
<br>
grid =<br>
xgrid: [1x31 double]<br>
ygrid: [1x36 double]<br>
zgrid: [1x30 double]<br>
dim: [31 36 30]<br>
pos: [33480x3 double]<br>
inside: [12773x1 double]<br>
outside: [20707x1 double]<br>
<br>
anatpath2 = [unixANALYSEpath
'Matlab_scripts/fieldtrip-20140114/template/anatomy/single_subj_T1.nii']<br>
template_mri = ft_read_mri(anatpath2);<br>
<br>
cfg = [];<br>
cfg.parameter = 'stat';<br>
cfg.interpmethod = 'nearest';<br>
statplot2 = ft_sourceinterpolate(cfg,stat,
template_mri);<br>
<br>
the input is volume data with dimensions [91 109 91]<br>
Warning: sphereradius is not used for projmethod
'nearest'<br>
> In fieldtrip-20140114/private/interp_ungridded at
86<br>
In ft_sourceinterpolate at 216<br>
the call to "ft_sourceinterpolate" took 37 seconds and
required the additional allocation of an estimated 96 MB<br>
<br>
-- somehow anatomy structure is lost... ?!<br>
statplot2 =<br>
freq: 64.9309<br>
stat: [902629x1 double]<br>
pos: [902629x3 double]<br>
dim: [91 109 91]<br>
inside: [1x902629 double]<br>
outside: [1x0 double]<br>
unit: 'mm'<br>
cfg: [1x1 struct]<br>
<br>
cfg = [];<br>
cfg.method ='slice';<br>
cfg.nslices = 30<br>
cfg.funparameter = 'stat';<br>
% cfg.maskparameter = 'mask';<br>
cfg.maskparameter = cfg.funparameter;<br>
cfg.anaparameter = 'anatomy';<br>
cfg.opacitymap = 'rampup';<br>
ft_sourceplot(cfg, statplot2);<br>
the input is source data with 902629 positions on a [91
109 91] grid<br>
Warning: do not understand cfg.anaparameter, not
plotting anatomy\n<br>
> In ft_sourceplot at 350<br>
the call to "ft_sourceplot" took 2 seconds and required
the additional allocation of an estimated 3 MB<br>
<br>
-- If using fieldtrip_new on server<br>
--> revision = '$Id: ft_sourceinterpolate.m 10221
2015-02-12 08:28:20Z roboos $';<br>
<br>
cfg =<br>
parameter: 'stat'<br>
interpmethod: 'nearest'<br>
statplot1 = ft_sourceinterpolate(stat, template_mri)<br>
Undefined function or variable 'abort'.<br>
Error in ft_sourceinterpolate (line 106)<br>
if abort<br>
<br>
-- <br>
________________________________________________________________________________________________________________________________________<br>
Heng-Ru May Tan<br>
Centre for Cognitive Neuroimaging (CCNi) ▫Institute of
Neuroscience and Psychology (INP) ▫<br>
College of Medical, Veterinary and Life Sciences &
College of Science and Engineering ▫ University of
Glasgow ▫<br>
58 Hillhead Street, Glasgow G12 8QB, United Kingdom ▫
+44 (0)141-330-5090 ▫ <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:Heng-RuMay.Tan@glasgow.ac.uk">
Heng-RuMay.Tan@glasgow.ac.uk</a><br>
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