No subject

Thu Jul 8 15:30:41 CEST 2010

Dear Jan-Mathijs,

Thank you so much for your help, that did the trick (see attached screenshot). I didn't realized that I could use the output from ft_volumerealign as the mri in ft_sourceinterpolate (or just overwrite the .transform of the mri). I will document all of my steps.

Thank you!
-Tony
________________________________________
From: FieldTrip discussion list [FIELDTRIP at NIC.SURFNET.NL] On Behalf Of jan-mathijs schoffelen [jan.schoffelen at DONDERS.RU.NL]
Sent: Thursday, July 08, 2010 7:52 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP]

Dear Tony,

What you did for the creation of the volume conduction model is indeed
correct. The question now is whether you also used the updated mri for
ft_sourceinterpolate, or whether you went back to loading the mri from
file without the correct coordinate frame info...

JM

On Jul 8, 2010, at 2:50 PM, Passaro, Antony D wrote:

> Dear Jan-Mathijs,
>
> Thank you again for your help, I appreciate it. I had forgotten to
> mention that I had used ft_volumerealign to align the mri before
> creating the volume conduction model using ft_preapre_singleshell. I
> then used the resulting vol in the ft_sourceanalyses, although I
> feel as though I am missing a step here which places the data in the
> same space as the MRI via the volume conduction model.
>
> Thanks,
> -Tony
> ________________________________________
> From: FieldTrip discussion list [FIELDTRIP at NIC.SURFNET.NL] On Behalf
> Of jan-mathijs schoffelen [jan.schoffelen at DONDERS.RU.NL]
> Sent: Thursday, July 08, 2010 7:14 AM
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: [FIELDTRIP]
>
> Dear Tony,
>
> It looks as if the coordinate system attached to your single subject's
> mri is not according to 4D's convention (it rather looks as if it is
> defined an mni space). The reason why I think this is that your x and
> y axes seem to be swapped, and there is a slight shift in the z-
> direction, suggesting a difference in origin. You can enforce the
> correct coordinate system onto the MRI by using ft_volumerealign in
> the interactive mode (and then specifying lpa, rpa and nasion by hand:
> this should return an updated mri.transform, which describes the
> transformation from voxel space to subject's headspace) . This should
> of course be done before calling ft_sourceinterpolate.
>
> Cheers,
>
> Jan-Mathijs
>
> On Jul 8, 2010, at 1:57 PM, Passaro, Antony D wrote:
>
>> Hi Arjen,
>>
>> Thank you very much for your help. I had not added the .pos and .dim
>> to my grid before interpolating, but after adding that information I
>> had the same result as before. I then checked the .pos and .dim of
>> the data before redefining it and noticed that it was already
>> identical to the template grid information. I also referred to the
>> example that you had suggested, however, I am currently looking at a
>> single subject to verify localization before moving on to multiple
>> subject analyses. Additionally, I would like to visualize data
>> projected on to a single subject's MRI prior to normalizing the
>> data. Any other suggestions would be greatly appreciated.
>>
>> Thank you again,
>> -Tony
>> ________________________________________
>> From: FieldTrip discussion list [FIELDTRIP at NIC.SURFNET.NL] On Behalf
>> Of a.stolk at fcdonders.ru.nl [a.stolk at FCDONDERS.RU.NL]
>> Sent: Thursday, July 08, 2010 4:17 AM
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: [FIELDTRIP]
>>
>> Hi Tony,
>>
>> Just to be sure; did you add the .pos and .dim from the template
>> grid to your data before interpolating?
>>
>> In code;
>>
>> data.pos = template_grid.pos;
>> data.dim = template_grid.dim;
>> cfg = [];
>> cfg.parameter = 'all';
>> data_int = ft_sourceinterpolate(cfg, data, mri);
>>
>> You can then ft_sourceplot the interpolated data.
>>
>> Best,
>> Arjen
>>
>> p.s. if still running into problems, make sure you have followed the
>> steps described here:
>> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space
>>
>> ----- Original Message -----
>> From: "Antony D Passaro" <Antony.Passaro at UTH.TMC.EDU>
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Sent: Thursday, July 8, 2010 10:41:11 AM GMT +01:00 Amsterdam /
>> Berlin / Bern / Rome / Stockholm / Vienna
>> Subject: [FIELDTRIP]
>>
>> Hi,
>>
>> I've been having issues projecting source estimates onto an MRI. I
>> discovered that several of my components (vol, grad, grid) did not
>> exist in the same coordinate space. Some were in mm and some in cm.
>> After I resolved these issues, I was able to use headmodelplot to
>> verify that everything was correct (see attached screenshot). I then
>> attempted source localization using lcmv and noticed that that the
>> projected activation existed in the incorrect orientation (see
>> second attached screenshot). I'm not sure what I'm doing wrong as
>> all of my components are in the correct space. I also tried to use
>> the interactive option of sourceplot to correctly set n,l,r but that
>> didn't seem to change anything. I'm sure it is something very simple
>> that I am overlooking but any help would be much appreciated.
>>
>> Thank you,
>> -Tony
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3668063
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3668063

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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