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Hi Fieldtrippers<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>
<br>
<blockquote type="cite">%%Source interpolate strangeness<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>
<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>
</blockquote>
<br>
<br>
<br>
<br>
<br>
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<div class="WordSection1">
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">_________________________________________________________________________________________________________________________________________<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span class="SpellE"><span
style="font-size:7.5pt;color:#595959;
mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:#595959;
mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:100.0%;
mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">Heng</span></span><span
style="font-size:7.5pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">-Ru <i style="mso-bidi-font-style:normal">May</i>
Tan<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:7.5pt;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000""><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:7.5pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
minor-latin;color:#595959;mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:
#595959;mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:
100.0%;mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">Centre
for Cognitive Neuroimaging (<span class="SpellE">CCNi</span>)</span><span
style="font-size:7.5pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000""> </span><span
style="font-size:7.5pt;mso-bidi-font-family:
Calibri;mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">▫</span><span
style="font-size:7.5pt;color:#595959;
mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:#595959;
mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:100.0%;
mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">Institute of
Neuroscience and Psychology (INP) </span><span
style="font-size:7.5pt;
mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:#595959;
mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:#595959;
mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:100.0%;
mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">▫ <o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:7.5pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
minor-latin;color:#595959;mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:
#595959;mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:
100.0%;mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">College
of Medical, Veterinary and Life Sciences & College of
Science and
Engineering</span><span
style="font-size:7.5pt;color:#595959;mso-themecolor:
text1;mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000""> </span><span
style="font-size:7.5pt;mso-bidi-font-family:
Calibri;mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">▫ </span><span style="font-size:7.5pt;
color:#595959;mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:
#595959;mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:
100.0%;mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">University
of Glasgow </span><span
style="font-size:7.5pt;mso-bidi-font-family:Calibri;
mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;mso-themetint:
166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">▫ <o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:7.5pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
minor-latin;color:#595959;mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:
#595959;mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:
100.0%;mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">58 <span class="SpellE">Hillhead</span>
Street, Glasgow G12 8QB, United Kingdom</span><span
style="font-size:7.5pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000""> </span><span
style="font-size:7.5pt;mso-bidi-font-family:
Calibri;mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">▫ +44 (0)141-330-5090</span><span
style="font-size:7.5pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000""> </span><span
style="font-size:7.5pt;mso-bidi-font-family:
Calibri;mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">▫ <a class="moz-txt-link-abbreviated" href="mailto:Heng-RuMay.Tan@glasgow.ac.uk">Heng-RuMay.Tan@glasgow.ac.uk</a></span><span
style="font-size:7.5pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000""><o:p></o:p></span></p>
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