[FieldTrip] Is there an error in my anatomical pipeline?

["Jörn M. Horschig"]

We got Adobe Photoshop at our institute ;)

Actually, I think it would be good to implement a cfg.flipimage option 
to ft_sourceplot. However, people should only use it when they know what 
they are doing and not just flip because it looks nicer :) Maybe we 
should discuss that in the next FT meeting in two weeks.


Greetings,
Jörn

On 4/4/2013 2:53 PM, Eelke Spaak wrote:
> Awesome, thanks a lot Jörn!
>
> I didn't think to check the numbers, newbie mistake... :) Now all
> that's left is to find an easy way to flip the image, but I imagine
> that shouldn't be too hard. Or just label the axes, I guess.
>
> On 4 April 2013 14:38, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:
>> Hi Eelke,
>>
>> the peak is on the left, don't be fooled by what you see. Trust the numbers
>> :)
>>
>> The x-coordinate that is given back is in MNI coordinates and is negative.
>> Since in MNI space, the x-axis goes to the right, this means that you are at
>> the left side of the brain.
>> See also this awesome appendix of an even greater tutorial:
>> http://fieldtrip.fcdonders.nl/tutorial/beamformingextended#appendixcomputation_of_virtual_meg_channels_in_source-space
>> (scroll down til 'We will now determine the positions on which...') :)
>>
>> Greetings
>> Jörn
>>
>>
>> On 4/4/2013 2:18 PM, Eelke Spaak wrote:
>>
>> Dear FieldTrippers,
>>
>> I am trying to do source reconstruction, but am encountering two weird
>> things in my pipeline related to anatomy. It could be that everything
>> is OK, but I am worried I might have introduced a left/right flip
>> somewhere.
>>
>> To read in my (dicom) MRI, I use:
>>
>> % read the mri
>> fprintf('loading mri for subject %d...\n', subjects(k).id);
>> mri = ft_read_mri(fetchDicomFilename(subjects(k).id));
>>
>> and then I mark the fiducials as follows:
>>
>> % align to fiducials in CTF coordsys
>> cfg = [];
>> cfg.coordsys = 'ctf';
>> cfg.method = 'interactive';
>> cfg.clim = [0 800];
>> mri = ft_volumerealign(cfg, mri);
>>
>> In attachment ft_volumerealign.png I show the plot that comes up.
>> Although the position of the different slices is not what I usually
>> expect, this should all still be fine, right? The yellow crosshair is
>> in the right fiducial location, as evidenced by the white blob below
>> the ear (which is always on the right hand side during MRI
>> acquisition).
>>
>> After marking r, l and n (and quitting with 'q') I do:
>>
>> % reslice to make everything right-side up
>> mri = ft_volumereslice([], mri);
>>
>> In attachment ft_sourceplot-1.png I show output of
>> ft_sourceplot([],mri) after this step. Note that the positions of the
>> axial/coronal/sagittal slices are not what one would typically expect.
>> Also note (and this is problem 1) that the right hand side of the
>> anatomy is displayed on the right hand side in the bottom (axial)
>> slice, but on the left hand side in the top right (coronal) slice.
>> Initially I thought this was just a benign visualisation issue
>> (analogous to
>> http://fieldtrip.fcdonders.nl/faq/my_mri_is_upside_down_is_this_a_problem),
>> but it might be a real problem after all, because of what I found
>> next.
>>
>> After these steps, I proceed to do segmentation and I create a headmodel:
>>
>> cfg = [];
>> cfg.coordsys = 'ctf';
>> mri = ft_volumesegment(cfg, mri);
>>
>> % make single shell model
>> cfg = [];
>> cfg.method = 'singleshell';
>> headmodel = ft_prepare_headmodel(cfg, mri);
>>
>> As outlined in the beamformingextended tutorial, I create a
>> subject-specific source model which I inverse-warp to MNI:
>>
>> % load template sourcemodel (grid) in mni space
>> template = load('~/ft-src/template/sourcemodel/standard_sourcemodel3d8mm');
>>
>> % warp the grid
>> cfg = [];
>> cfg.grid.warpmni = 'yes';
>> cfg.grid.template = template.sourcemodel;
>> cfg.grid.nonlinear = 'yes';
>> cfg.mri = mri;
>> sourcemodel = ft_prepare_sourcemodel(cfg);
>>
>> (See attachment grid-hdm-grad.png for a plot of all three geometrical
>> objects superimposed. Looks fine to me.) Then I create a leadfield:
>>
>> cfg = [];
>> cfg.grid = sourcemodel;
>> cfg.vol = headmodel;
>> cfg.channel = {'MEG'};
>> cfg.grad = data.grad;
>> leadfield  = ft_prepare_leadfield(cfg, data);
>>
>> The next step, which is the one which alerted me to the potential
>> problem in the steps above, is to do an LCMV beamformer on a small
>> time window of my ERF:
>>
>> % compute ERF covariance in small window
>> cfg = [];
>> cfg.covariance = 'yes';
>> cfg.covariancewindow = [1.5 1.55];
>> tl_right = ft_timelockanalysis(cfg, rightErf);
>>
>> % do beamforming
>> cfg = [];
>> cfg.method = 'lcmv';
>> cfg.grid = leadfield;
>> cfg.vol = headmodel;
>> cfg.lcmv.lambda = '5%';
>> cfg.lcmv.projectnoise = 'yes';
>> cfg.lcmv.keepfilter = 'yes';
>>
>> sourceRight = ft_sourceanalysis(cfg, tl_right);
>>
>> % normalise with noise
>> sourceRightNAI = sourceRight;
>> sourceRightNAI.avg.pow = sourceRight.avg.pow ./ sourceRight.avg.noise;
>>
>> % copy over pos and dim from template
>> sourceRight.pos = template.sourcemodel.pos;
>> sourceRight.dim = template.sourcemodel.dim;
>> sourceRightNAI.pos = template.sourcemodel.pos;
>> sourceRightNAI.dim = template.sourcemodel.dim;
>>
>> % interpolate onto template brain
>> cfg              = [];
>> cfg.voxelcoord   = 'no';
>> cfg.parameter    = 'avg.pow';
>> cfg.interpmethod = 'nearest';
>> cfg.coordsys     = 'mni';
>> sourceRight_int= ft_sourceinterpolate(cfg, sourceRight, template_mri);
>> sourceRightNAI_int= ft_sourceinterpolate(cfg, sourceRightNAI, template_mri);
>>
>> % plot
>> cfg              = [];
>> cfg.funparameter = 'avg.pow';
>> cfg.method       = 'ortho';
>> cfg.location     = 'max';
>> cfg.coordsys = 'mni';
>> ft_sourceplot(cfg, sourceRightNAI_int);
>>
>> The output of the above step is shown in ft_sourceplot-2.png. Note
>> that there clearly is a maximum in the posterior right hemisphere. Now
>> compare this to when I just plot the sensor-level ERF for the same
>> time interval:
>>
>> c2=[];
>> c2.layout='CTF275.lay';
>> c2.xlim = [1.5 1.55];
>> figure;ft_topoplotER(c2,rightErf);
>>
>> (See attachment ft_topoplotER.png.) The sensor-level ERF looks to me
>> as if there should be a dipole in the left hemisphere. (That's problem
>> 2.)
>>
>> Now of course I know that interpreting axial gradient data by eye is
>> difficult, but this left-side increase is present in the majority of
>> my subjects, yet the resulting LCMV maximum always ends up in the
>> right hemisphere. Therefore my question: am I doing something wrong in
>> my anatomical pipeline, causing a left-right flip? An indication that
>> this might be the case is the weird display in ft_sourceplot after my
>> ft_volumereslice step. Or is it really possible that for many
>> subjects, a left-sided sensor topography ends up in the right
>> hemisphere after beamforming? (My intuitions on this are not very
>> strong.)
>>
>> Apologies for the lengthy e-mail. I thought it wise to provide all
>> possible details :) Hopefully someone can help me!
>>
>> Best,
>> Eelke
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail: jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web: http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands