[FieldTrip] Interpolate, normalise and sourcegrandaverage with MNE
Marc Recasens
recasensmarc at gmail.com
Wed Mar 16 01:48:16 CET 2016
Dear JM
Thanks for you answer! didn't know anything about Connectome Workbench, but
this FieldTrip-Connectome link sounds VERY cool! I'll have a look at the
wb_command and see if I can read the Conte69 *surf from there.
Best wishes
Marc
On Tue, Mar 15, 2016 at 3:16 PM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:
> Marc,
>
> I would not recommend to try and create a low-resolution mesh for Colin’s
> brain. In some sense, Colin’s brain is not more special than any of your
> single subject brains. In other words, you could pick any of your single
> subjects, and use that for visualization.
> If you would like to visualize your results on a ‘average’ brain, I’d
> recommend the Conte69 brain, that has been developed at Washington
> University (the Caret people).
>
> As a side note, Caret development is discontinued by the WashU group. They
> have moved to connectome workbench, which has most of the functionality
> supported by Caret. Specfically, there’s now also a freesurfer_to_fs_LR
> script that uses wb_command (the command line utility of connectome
> workbench). Note 2: the *.coord.* and *.topo.* files are old style Caret.
> Nowadays, the topologies are represented in a single file *.surf.* (rather
> than the positions in the coord and the triangles in the topo).
>
> BEst,
> JM
>
>
>
>
> On 14 Mar 2016, at 23:09, Marc Recasens <recasensmarc at gmail.com> wrote:
>
> 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);
>> >>
>> >> %%%%%%%%%%%%%%
>> >>
>> >>
>> >> _______________________________________________
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>> >> fieldtrip at donders.ru.nl
>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> >
>> >
>> >
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>
>
>
> --
> Marc Recasens
> Tel.: +34 639 24 15 98
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>
>
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--
Marc Recasens
Tel.: +34 639 24 15 98
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