[FieldTrip] MNE tutorial

[Bruno L. Giordano]

Sorry, my replies were not meant for the list.
On May 2, 2013 8:28 AM, "Bruno L. Giordano" <brungio at gmail.com> wrote:

> Ah, I just saw that your problem might be with the origin of the
> anatomical space. Have you tried to see what happens if you set its origin
> to the anterior commissure before giving it in input to field trip?
> On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:
>
>>  Running the full Freesurfer reconstruction pipeline (without the hybrid
>> skull stripping and Talaraich alignment on the fieldtrip side) appears to
>> have been successful.
>>
>> However, when I try to continue with the tutorial I find that my volume
>> and source grid don't line up (even before any issues converting to sensor
>> space):
>>
>> Figure: http://imgur.com/uo9uPUc (code below)
>>
>> Does anyone have any idea what could be wrong?
>>
>> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
>> suite)?
>> If it is in talairach coordinates, how do I load the Talairach aligned
>> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>>
>> Do I need to manually include the transform from transform/talairach.xfm?
>> To include that can I use it directly as mri.transform in fieldtrip or do I
>> need to multiply it by the existing mri.transform which is there when
>> loading the raw anatomy scan (.img)? Come to think of it what does that
>> transform represent?
>>
>> Sorry if these are not fieldtrip questions but I am trying to follow the
>> fieldtrip MNE tutorial so I was hoping someone might know.
>>
>> Thanks
>>
>> Robin
>>
>> % load freesurfer image
>> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
>> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
>> % load MNE grid% computed with mne_setup_source_space --ico -6
>> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
>> sourcespace = ft_convert_units(bnd, 'cm');
>> % Volume conduction model
>> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
>> seg = ft_volumesegment(cfg, mri_fs_tal);
>> cfg = [];cfg.method = 'singleshell';
>> vol = ft_prepare_headmodel(cfg, seg);
>> % Check volume conduction
>> figure; hold on
>> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
>> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>>
>> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>>
>> I am trying to run through the MNE tutorial here:
>>
>> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>>
>> Unfortunately after the volumetric processing in freesurfer my
>> intermediate result looks wrong.
>>
>> I have followed the steps (including interactive alignment to
>> Talairach) according to the tutorial. I wondered if anyone has any
>> idea what could be wrong, or could point to some more possible
>> diagnostic commands to run?
>>
>> The original Subject01.mgz file seems to have been saved correctly.
>> But if I load the orig.mgz created with:
>> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
>> and plot it with ft_sourceplot it has the same offset and upside down
>> position as the final incorrectly segments freesurfer image. Could
>> this indicate a problem?
>>
>> Thanks for any help,
>>
>> Cheers
>>
>> Robin
>>
>>
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>
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