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Date: Tue, 22 Jan 2008 17:01:45 -0500
From: greve@nmr.mgh.harvard.edu
To: dhaglerjr@hotmail.com
Subject: Re: [Freesurfer] Creating average overlays for time-varying data (MEG)
CC: p.kitterick@psych.york.ac.uk; freesurfer@nmr.mgh.harvard.edu

Hi Don, have you tried using mri_surf2surf with  --mapmethod nnf ? That will prevent the interpolation and map each ico4 to the nearest ico7.

doug

Don Hagler wrote:

If you have problems writing out mgh files with 140000x1x1x500 volumes, maybe you need more memory (>=2GB?).  Or a 64 bit machine?  Or you could downsample your time courses if you haven't already.

I do use matlab to convert decimated source time course files (stc) to mgh.  Before writing out the mgh file, I do sparse smoothing (10+ steps) followed by regular smoothing (10+ steps) on each frame.  It is slow, but works fine on 64 bit machines with 2GB RAM.  It probably works on 32 bit machines too, but I haven't used one in awhile.  The largest number of frames I've tried is 450.

Resampling to ico7 for group averaging is straightforward with mri_surf2surf.  I do group analysis one frame at time to conserve memory.

I don't think using mri_surf2surf to resample sparse data to ico4 (for example) would work well because of interpolation with neighboring zero values (but I haven't tried it).

An option that I am considering is to start with ico4 vertices and sample them to each subject in order to choose which vertices should be the set of "decimated" dipoles.  The complication here is that mri_surf2surf does not give a one-to-one mapping between ico vertices and single subject vertices.  I think it would be necessary to derive a look-up-table for each subject to provide such a one-to-one mapping.  Then the ico resampling would be done not with mri_surf2surf, but with a matlab script that consults the look-up-table.

For display purposes, I guess you would still need to create an ico4 average subject.

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> Date: Mon, 21 Jan 2008 16:08:41 -0500
> From: greve@nmr.mgh.harvard.edu
> To: p.kitterick@psych.york.ac.uk
> Subject: Re: [Freesurfer] Creating average overlays for time-varying data (MEG)
> CC: freesurfer@nmr.mgh.harvard.edu
>
>
>
> Pádraig Kitterick wrote:
>
> > Dear list,
> >
> > I am trying to use freesurfer to visualise MEG data (minimum norm)
> > overlayed on the cortical surface, both at an individual and group
> > level. I have successfully processed all of the participants MRIs
> > using recon-all, and have decimated the cortical surface (white) to
> > compute the MEG solution. I would be grateful if anyone could help
> > with the following issues I have run into:
> >
> > 1) I would like to know how to view the time-varying solution over the
> > cortex using tksurfer. I have successfully exported the overlay for a
> > single sample to a .w file (using matlab), and then smoothed it
> > (mri_surf2surf) and viewed it on the cortical surface, which works
> > great. But I am aware that .w format only supports a single 'frame' of
> > data. Some previous posts on the list suggest that exporting the data
> > in .mgh format as a nverts x 1 x 1 x nsamples volume would allow
> > visualisation of the timecourse in tksurfer.
> >
> > My question is: is there a way to only write out the data for the
> > vertices with values (i.e. left after decimation) when using the mgh
> > format, and not a matrix of the total vertices in the original cortex?
> > For example, if the surface has N vertices, and after decimation I
> > have M vertices left, using the .w format I only need to write out
> > data for the M vertices, along with a list of the vertex numbers to
> > place them on the original surface. Can I do this with .mgh? It is
> > difficult to get matlab to write out an mgh file with a 140000x1x1x500
> > volume!
>
> You can't do this with the mgh format. You can use compressed mgh (mgz),
> and that will compress all the 0s, but that probably does not take you
> where you need to be. How are you decimating your data? One way would be
> to create a decimated average subject with a lower order icosahedron and
> then use that as the target for mri_surf2surf.
>
> >
> > 2) I wish to view the average data across several subjects, mapped
> > onto the fsaverage subject template. I have seen that mris_preproc can
> > warp one or more overlays onto a single subject. My question is: will
> > mris_preproc work with the type of .mgh files I described above, i.e.
> > containing multiple frames of data overlay? Or am I better trying to
> > do the whole operation with .w files, with one per timepoint?
>
> You can do it with multiple frame input (though the output frames will
> be a stack of original frames from all the subjects).
>
> doug
>
> >
> > Many thanks in advance,
> >
> > Padraig
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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