Hi Doug,
No, I haven't tried it for this, but I have read the help before. It says this: "If nnf is chosen, then the value at the target vertex is set to that of the closest source vertex."
If you wanted to go from a sparsely valued single subject surface (i.e. decimated dipoles) to ico4, it seems that you would probably miss many of your dipole vertices because they wouldn't necessarily be the ones closest to the ico4 vertices. Going from decimated dipoles to ico7 may work ok, although you may still miss a few dipoles, which is why smoothing before sampling to ico seems to be a good idea. And we have to smooth anyway before doing group analysis because the ico7 vertices that correspond to a single subject's decimated dipoles will vary from subject to subject.
If we chose our decimated dipoles based on ico4, we do could group analysis without any smoothing on a much smaller number of vertices.
Don
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.
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:
- 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.
- 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
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