[FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Fri May 8 13:38:48 CEST 2015


Have you ensured that the stat.pos field contains the dipole positions, coregistered to the template brain?


On May 8, 2015, at 1:22 PM, Heng-Ru May Tan <Heng-RuMay.Tan at glasgow.ac.uk<mailto:Heng-RuMay.Tan at glasgow.ac.uk>> wrote:

Hi Fieldtrippers

[The previous email didn't display properly so resending this again.]

I am having trouble running ft_sourceinterpolate... I didn't seem to have this issue before. =(
The anatomy seems to be missing and so when I subsequently call ft_sourceplot, the brain anatomy is not 'available' for plotting.
Here are some example of the things I tried and the errors in hope that someone might be able help!

Many thanks in advance,

-- this is a stat structure used:

stat =
    prob: [33480x1 double]
    cirange: [33480x1 double]
    mask: [33480x1 logical]
    stat: [33480x1 double]
    ref: [33480x1 double]
    df: 185
    critval: [-1.9729 1.9729]
    dim: [33480 1]
    inside: [10354x1 double]
    outside: [23126x1 double]
    pos: [33480x3 double]
    freq: 64.9309
    cfg: [1x1 struct]

grid =
    xgrid: [1x31 double]
    ygrid: [1x36 double]
    zgrid: [1x30 double]
    dim: [31 36 30]
    pos: [33480x3 double]
    inside: [12773x1 double]
    outside: [20707x1 double]

anatpath2 = [unixANALYSEpath 'Matlab_scripts/fieldtrip-20140114/template/anatomy/single_subj_T1.nii']
template_mri = ft_read_mri(anatpath2);

cfg = [];
cfg.parameter = 'stat';
cfg.interpmethod  = 'nearest';
statplot2 = ft_sourceinterpolate(cfg,stat, template_mri);

the input is volume data with dimensions [91 109 91]
Warning: sphereradius is not used for projmethod 'nearest'
> In fieldtrip-20140114/private/interp_ungridded at 86
In ft_sourceinterpolate at 216
the call to "ft_sourceinterpolate" took 37 seconds and required the additional allocation of an estimated 96 MB

-- somehow anatomy structure is lost... ?!
statplot2 =
    freq: 64.9309
    stat: [902629x1 double]
    pos: [902629x3 double]
    dim: [91 109 91]
    inside: [1x902629 double]
    outside: [1x0 double]
    unit: 'mm'
    cfg: [1x1 struct]

cfg = [];
cfg.method  ='slice';
cfg.nslices  = 30
cfg.funparameter  = 'stat';
%         cfg.maskparameter = 'mask';
cfg.maskparameter = cfg.funparameter;
cfg.anaparameter = 'anatomy';
cfg.opacitymap    = 'rampup';
ft_sourceplot(cfg, statplot2);
the input is source data with 902629 positions on a [91 109 91] grid
Warning: do not understand cfg.anaparameter, not plotting anatomy\n
> In ft_sourceplot at 350
the call to "ft_sourceplot" took 2 seconds and required the additional allocation of an estimated 3 MB

-- If using fieldtrip_new on server
--> revision = '$Id: ft_sourceinterpolate.m 10221 2015-02-12 08:28:20Z roboos $';

cfg =
parameter: 'stat'
interpmethod: 'nearest'
statplot1 = ft_sourceinterpolate(stat, template_mri)
Undefined function or variable 'abort'.
Error in ft_sourceinterpolate (line 106)
if abort

Heng-Ru May Tan
Centre for Cognitive Neuroimaging (CCNi) ▫Institute of Neuroscience and Psychology (INP) ▫
College of Medical, Veterinary and Life Sciences & College of Science and Engineering ▫ University of Glasgow ▫
58 Hillhead Street, Glasgow G12 8QB, United Kingdom ▫ +44 (0)141-330-5090 ▫ Heng-RuMay.Tan at glasgow.ac.uk<mailto:Heng-RuMay.Tan at glasgow.ac.uk>
<mailto:Heng-RuMay.Tan at glasgow.ac.uk>
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>

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