[FieldTrip] Interpolate, normalise and sourcegrandaverage with MNE
Marc Recasens
recasensmarc at gmail.com
Mon Mar 14 23:09:36 CET 2016
Dear Jan-Mathijs, Sara and FT community,
I'd like to bring up this old thread which I think might be of interest us
all. I don't know if there's been any new development on the MNE approach
(?) since this thread was started one year ago. Anyway, in order to get
template-registered surfaces that allow for inter-subject
comparison/averaging, I tried using Jan-Mathijs suggestion to post-process
the surfaces that come out of the freesurfer pipeline according to the
recipe described on
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR
.
- I managed to get the .coord and .topo files using CARET
- I managed to create 8196 pnt mesh ( using "mne_setup_source_space --ico
-6") registered to the template (fsaverage I assume) using the following
files. Actually I'm not 100% sure these are the correct files I should read
(the output seems to make sense though):
ft_read_headshape({[%SubjectID.%Hemisphere.164k_fs_LR.topo.gii']
[%SubjectID.%Hemisphere.midthickness_orig.164k_fs_LR.coord.gii']}); % for
rh/lh.orig
ft_read_headshape({[%SubjectID.%Hemisphere.164k_fs_LR.topo.gii']
[%SubjectID.%Hemisphere.sphere.164k_fs_LR.coord.gii']}); % for rh/lh.sphere
ft_read_headshape({[%SubjectID.%Hemisphere.164k_fs_LR.topo.gii']
[%SubjectID.%Hemisphere.white_orig.164k_fs_LR.coord.gii']}); % for
rh/lh.white (JM did not say anything about rh/lh.white but
mne_setup_source_space required it)
- I got the resulting template-registered sourcespace properly
co-registered in the correct coordinate system (individual sensor space)
- and successfully applied MNE on the template-registered sourcespace.
Sources make sense are meshes are exchangeable across subjects (which I
think makes sense since they're all registered to a template).
HOWEVER, I'm stuck in what I think should be a rather straight forward
step, which is the creation of a template sourcemodel/grid (from the
fsaverage or Colins brain) that I can use in the same way as the
MNI-aligned template grid is used; that is a Talairach aligned surface with
8196 pnts that I can. I tried to use the 'cortex_8196.surf.gii' like in the
lines below, but without success (because of MNI instead of TAL aligned?):
template_sourcemodel = ft_read_headshape('cortex_8196.surf.gii');
template_sourcemodel = ft_convert_units(template_sourcemodel, 'cm');
bnd.pnt = template_sourcemodel.pnt;
bnd.tri = template_sourcemodel.tri;
Any ideas about how to get such a template mesh will be highly appreciated!
Best wishes
Marc
On Thu, Oct 1, 2015 at 4:07 PM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:
> Hi Sara,
>
> What you need are some of the .coord files, and the .topo files.
>
> Specifically, the midthickness_orig and the sphere files should be
> converted into a format that the mne-software can work with.
> The only way I managed this, was to convert the gifti files back into
> freesurfer’s format:
>
> tmp = ft_read_headshape({‘something-something.topo.gii’
> ‘somethingelse-.L.midthickness_orig.coord.gii’});
> ft_write_headshape(‘lh.orig’, tmp, ‘format’, ‘freesurfer’);
>
> and likewise for the right hemisphere, as well as for the spheres.
>
> Then, you can proceed with using mne_setup_source_space to create the 8196
> mesh. The final tricky thing eventually is to get the stuff properly
> co-registered in the correct coordinate system again, but this should
> proceed in the same way as when you would have used non-surface registered
> meshes.
>
> The creation of the volume conduction model is a separate step (and does
> not require the cortical meshes).
>
> Best,
> Jan-Mathijs
>
>
> On Oct 1, 2015, at 4:48 PM, Sara Aurtenetxe <s.aurtenetxe at bcbl.eu> wrote:
>
> > Dear Jan Mathijs,
> >
> > Thank you very much for your quick and detailed answer!
> >
> > As suggested, I post-processed the surface of one of my subjects based
> on the recipe on the link.
> > The process resulted into a bunch of files (e.g. .L.164k_fs_L.topo.gii,
> .L.white_mni.164k_fs_LR.coord.gii, .L.def_sphere.164k_fs_L.coord.gii),
> > but at this point I am not sure about how to proceed. So I have now
> several questions:
> >
> > - Do you know which are the files containing the registered data for the
> creation of the meshes?
> > How should I create them given the current format? most are .gii files.
> > - Once creating the meshes, should I follow with the creation of the
> volume conduction model
> > and analysis of the functional data as described in the tutorial?
> http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> >
> > Apologize for all these specific questions but it is being a little bit
> confusing to me.
> > So if anyone has experienced the same and/or have any suggestion, any
> comment would be very welcomed.
> >
> > Thanks a lot in advance,
> >
> > Best,
> >
> > Sara
> >
> >
> >
> >
> >
> >
> >
> > ----- Original Message -----
> > From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> > To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> > Sent: Wednesday, September 30, 2015 9:33:03 AM
> > Subject: Re: [FieldTrip] Interpolate, normalise and sourcegrandaverage
> with MNE
> >
> > Hi Sara,
> >
> > I think that in this case there is no absolutely ‘correct’ approach,
> although some approaches may make more sense than others.
> > At this point in time it is indeed not well documented how to proceed
> from individual subject results source-reconstructed onto an individual
> cortically constrained mesh to a group analysis.
> > In the past, we have been working with a procedure where the surface
> data were interpolated onto a 3D-grid so that we could use volumetric
> normalization techniques in order to get the subjects into a common space
> to allow for group statistics. So, here the order of the steps would be to
> call ft_sourceinterpolate, followed by ft_volumenormalise, or to
> interpolate the functional data directly onto a MNI-warped grid (
> http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space
> ).
> > In the code you pasted in your e-mail message, there is also reference
> to ft_volumerealign, but I am not sure I understand why this is a required
> step at this point in the pipeline.
> >
> > All the above being said, nowadays I would advocate a slightly different
> approach, which bypasses the volumetric interpolation, where per subject I
> would use cortical meshes that is surface-registered to a template mesh,
> which as a consequence allows for direct comparison of source locations
> across subjects. The way to achieve this would be to post-process the
> surfaces that come out of the freesurfer pipeline according to the recipe
> described on
> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR.
> After this registration step, the low-resolution (i.e. in this case the
> 8196-vertex) meshes can be created.
> >
> > Best wishes,
> > Jan-Mathijs
> >
> >
> >
> >
> > Jan-Mathijs Schoffelen, MD PhD, Senior researcher
> >
> > Max Planck Institute for Psycholinguistics
> > Donders Centre for Cognitive Neuroimaging
> >
> > E-mail: j.schoffelen at donders.ru.nl
> > Telephone: +31-24-3614793
> >
> > http://www.fieldtriptoolbox.org
> > http://www.hettaligebrein.nl
> >
> >
> >
> > On Sep 29, 2015, at 5:27 PM, Sara Aurtenetxe <s.aurtenetxe at bcbl.eu>
> wrote:
> >
> >> Dear all,
> >>
> >> I am working on the source analysis of ERF data from ElektaNeuromag
> system, with individual T1s, using minimum-norm estimate as described in
> the following tutorial:
> >> http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> >> I am exactly following the suggested steps, and so got the source
> estimation for each of my subjects (bellow the output for one subject),
> which i can nicely plot with the ft_plot_mesh function:
> >>
> >> sourceest =
> >>
> >> time: [1x1401 double]
> >> inside: [8196x1 logical]
> >> pos: [8196x3 double]
> >> method: 'average'
> >> avg: [1x1 struct]
> >> cfg: [1x1 struct]
> >>
> >> Now, prior to a ft_sourcegrandaverage and ft_sourcestatistics,
> >> I am trying to normalise (ft_volumenormalise) and interpolate
> (ft_sourceinterpolate) the functional and anatomical data.
> >>
> >> However, I am struggling in this two last steps.
> >> Since I did not find a clear pipeline/tutorial about the exact approach
> (am I missing something?)
> >> and after trying several options (bellow I copy the code I am using),
> it is not clear to me:
> >>
> >> - which is the exact input data for each of these last two functions,
> and
> >> - in which order they should be called.
> >>
> >> Now, I would highly appreciate if anyone could give me any cue about
> which the correct approach is.
> >>
> >> Thank you in advance,
> >>
> >> All the best,
> >>
> >> Sara
> >>
> >>
> >>
> >> %%%%%%%%%%%%
> >>
> >> % Inverse solution
> >> cfg = [];
> >> cfg.method = 'mne';
> >> cfg.grid = leadfield;
> >> cfg.vol = vol;
> >> cfg.mne.prewhiten = 'yes';
> >> cfg.mne.lambda = 3;
> >> cfg.mne.scalesourcecov = 'yes';
> >> cfg.senstype = 'MEG';
> >>
> >> sourceest = ft_sourceanalysis(cfg,erf);
> >>
> >> % read T1 volume - coords in scanner space
> >> mri = ft_read_mri('s01.nii');
> >> mri.coordsys = 'neuromag';
> >>
> >> % read headshape - Neuromag coords
> >> hsf = 's01.fif';
> >> [headshape] = ft_read_headshape(hsf);
> >>
> >> % align T1 with head posiiton in MEG
> >> cfg = [];
> >> cfg.method = 'headshape';
> >> cfg.parameter = 'anatomy';
> >> cfg.headshape.headshape = headshape;
> >> cfg.headshape.interactive = 'no';
> >>
> >> mri_real = ft_volumerealign(cfg,mri);
> >>
> >> % normalize the realinged individual MRI to SPM template
> >> cfg = [];
> >> cfg.spmversion = 'spm8';
> >> % cfg.template='T1.nii'; % when enabling this field, an incoming error
> message indicates that the template is not in the spm coordinate system.
> >> % However, is the one used by default in this
> function (as mentioned in the reference) so it is confusing to me
> >>
> >> norm_mri = ft_volumenormalise(cfg,mri_real);
> >>
> >> % interpolate Source with MEG-aligned T1
> >> cfg = [];
> >> cfg.parameter = 'all';
> >> cfg.downsample = 2;
> >>
> >> source_int = ft_sourceinterpolate(cfg, sourceest,norm_mri);
> >>
> >> %%%%%%%%%%%%%%
> >>
> >>
> >> _______________________________________________
> >> fieldtrip mailing list
> >> fieldtrip at donders.ru.nl
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >
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>
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--
Marc Recasens
Tel.: +34 639 24 15 98
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