[FieldTrip] reverse source interpolate?
Vitoria Piai
v.piai.research at gmail.com
Wed Mar 12 17:50:00 CET 2014
Dear Erick,
"simply label and/or define my ROI in the MNI grid. When I warp to the
individuals, everything is in place without a hitch" -> that sounds like
a good thing to do.
Is this a very complicated thing to do? Would you mind sharing a piece
of code or some tips for how I could achieve it?
Thanks once more, Vitória
On 3/12/2014 11:37 AM, Erick Ortiz wrote:
> Dear Vitoria,
>
> What I do usually, is to simply label and/or define my ROI in the MNI
> grid. When I warp to the individuals, everything is in place without a
> hitch.
>
> About the interpolation, I cannot help much more. I have been using my
> own tools for years, and I was not following the support of atlases in
> Fieldtrip.I tried it today, but had issues with coordinate system
> labeling when defining a ROI (I updated to the latest version by SVN):
>
> afni = ft_read_atlas('template/atlas/afni/TTatlas+tlrc.HEAD');
> cfg = [];
> cfg.method = 'ortho';
> cfg.interactive = 'yes';
> cfg.funparameter = 'coh';
> cfg.atlas = afni;
> cfg.coordsys = 'mni';
> % cfg.roi = 'Middle Temporal Gyrus';
> % cfg.inputcoord = 'tal';
> ft_sourceplot(cfg, interp);
>
> Also note that I had to use ft_read_atlas, because ft_prepare_atlas
> does not generate the brick0label/brick1label fields.
>
> It works well, but if I try to define a ROI (uncommenting the two
> lines), I get the error "The field cfg.inputcoord is required". There
> seems to be some confusion between inputcoord and coordsys.
>
> It can be because I was doing something wrong: maybe a Fieldtrip
> developer could comment on that?
>
> Best,
> Erick
>
>
>
> On Wed, Mar 12, 2014 at 9:24 AM, Vitoria Piai
> <v.piai.research at gmail.com <mailto:v.piai.research at gmail.com>> wrote:
>
> Dear Erick,
>
> Thanks for your detailed reply.
> I've been using individual MNI-warped grids (point 4 below) and
> I'm always using ft_convert_unit so those points are alright in my
> data.
>
> The reason why I do need to interpolate (at least, I think I
> need), is because I'm looking for max 'pow' in anatomically
> defined regions given the afni atlas. I managed to get it to work
> by interpolating to the mri and looking for max 'pow' given a
> label (e.g., 'Middle Temporal Gyrus') using ft_volumelookup.
> Do you have any experience with this approach (searching within
> anatomical labels) without having to interpolate?
>
> Thanks once more, Vitória
>
>
>
>
> On 3/11/2014 6:35 PM, Erick Ortiz wrote:
>> Dear Vitória and Cornelius,
>>
>> this is a common problem, and maybe it would be good to clarify
>> the strategies that can be used here. I hope this can help others
>> in a similar situation, which I have found many times.
>>
>> 1) You are trying to convert voxel indexes to head (CTF)
>> coordinates. In this case, there are two mistakes in the code:
>> 1a) pos = warp_apply( pinv( sourceNAIInt.transform ), posInt,
>> 'homogeneous' );
>> ... should be done with sourceNAIInt, not mri. The transforms are
>> different, in general; e.g. note the downsample=2.
>> 1b) use cfg.locationcoordinates = 'head', as commented by JM in a
>> previous post. Or remove this line, since 'head' is the default.
>>
>> 2) But if you are working with the same subject/grid, there is no
>> need for interpolation at all. Simply find the grid position with
>> highest 'pow' and take its position.
>> [dummy,ind] = max(source.avg.pow);
>> pos = source.pos(ind,:);
>>
>> 3) However, this is not possible when using different grids, e.g.
>> in a grand average in MNI coordinates. Find the peak ('pos') in
>> the interpolated volume, as in Cornelius' code, then find the
>> index of the nearest grid position for a common (again, MNI)
>> grid. This is also in JM's message.
>>
>> dpos = source.pos - repmat( pos, size(source.pos,1), 1 );
>> [dummy,ind] = min(sum(dpos.^2,2));
>>
>> 4) What I have been using, and strongly recommend, is an MNI grid
>> warped to the subject's anatomy, according to this procedure:
>> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space
>>
>> This would give you both the benefits of working in MNI
>> coordinates, and the ease of having a common grid across subjects
>> (for instance, enabling solution #2). Still, some projects do
>> call for one of the other options.
>>
>> Just a couple of details:
>> - Pay utmost attention to coordinate systems and units. For
>> instance, it is common to confuse unlabeled cm for mm, and either
>> of these with voxels. Try to also label all structures as CTF or
>> SPM (MNI).
>> - Using pinv instead of inv is usually a good idea. Here, it is a
>> not an issue, but matrix inversion in MATLAB can lead to a world
>> of hurt to the unwary.
>>
>> Best,
>> Erick
>>
>>
>>
>> On Tue, Mar 11, 2014 at 4:04 PM, Vitoria Piai
>> <v.piai.research at gmail.com <mailto:v.piai.research at gmail.com>> wrote:
>>
>> Dear FT-ers,
>>
>> I found an old posting to the mailing list (see below) that
>> never got answered so my question still holds: given a
>> location I found in the interpolated source, how do I find
>> back the same location in .pos of the non-interpolated data?
>> I can try and go around it by finding the corresponding MNI
>> coordinates in the interpolated data (which by now I have to
>> do by hand, so not optimal anyways), and then look for those
>> coordinates in .pos. But I was wondering, like Cornelius was
>> in his post, whether there is a neater way to get this
>> information.
>>
>> Thanks a lot for the help,
>> Vitória
>>
>>
>> >>>>>>>>>>>>>>
>>
>> Hi mailing list,
>>
>> I'm still struggling with the conversion of coordinates
>> between source and
>> interpolated source space.
>> For example, if i have the position of a single grid
>> point how do i get the
>> corresponding voxel in the interpolated source
>> structure. Or the other way
>> around, how to get the grid point which corresponds to a
>> voxel (e.g the max
>> voxel) in the interpolated source structure.
>>
>> I think this should be a common problem when working with
>> virtual
>> electrodes, shouldn't it?
>>
>> To make things easier i put together a example with the
>> data from the
>> source tutorial where i tried to calculated the grid pos
>> of the max voxel
>> in the interpolated source.
>>
>> clear all;
>> load sourcePost_nocon; % source structure from tutorial
>> mri = ft_read_mri('Subject01.mri'); % mri of subject01
>> from tutorial
>>
>> sourceNAI = sourcePost_nocon;
>> sourceNAI.avg.pow = sourcePost_nocon.avg.pow ./
>> sourcePost_nocon.avg.noise;
>> sourceNAI=rmfield(sourceNAI,'freq'); % had to remove that
>> to let
>>
>> cfg = [];
>> cfg.downsample = 2;
>> cfg.parameter = 'avg.pow';
>> sourceNAIInt = ft_sourceinterpolate(cfg, sourceNAI , mri);
>>
>> % Find position of max activity
>> [dum, maxindx] = max(sourceNAIInt.avg.pow(:));
>> [xi, yi, zi] = ind2sub(sourceNAIInt.dim, maxindx);
>> posInt=[xi, yi, zi];
>>
>> % Plot interpolated source with position of max activity
>> cfg = [];
>> cfg.method = 'ortho';
>> cfg.funparameter = 'avg.pow';
>> cfg.locationcoordinates = 'voxel';
>> cfg.location = posInt; % location of max
>> activity is marked
>> correctly.
>> figure;
>> ft_sourceplot(cfg,sourceNAIInt);
>>
>> % Transform coordinate back to uninterpolated source???
>> dpos = warp_apply(inv(mri.transform), posInt, 'homogeneous');
>>
>>
>> % Plot uninterpolated source with position aquired from
>> interpolated source
>> cfg = [];
>> cfg.method = 'ortho';
>> cfg.funparameter = 'avg.pow';
>> cfg.locationcoordinates = 'voxel';
>> cfg.location = dpos; % unfortunately this
>> coordinate is
>> obviously wrong!!! WHY?
>> figure;
>> ft_sourceplot(cfg,sourceNAI);
>>
>>
>> Unfortunately the solution of Jan Mathijs did not work,
>> nor did mine :(
>>
>> Any ideas???
>>
>> Cornelius
>>
>>
>>
>>
>>
>>
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>>
>>
>>
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