[FieldTrip] Question on tutorial http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Sun May 8 21:35:38 CEST 2016

Hi Parham,

> On 08 May 2016, at 19:07, parham hashemzadeh <ph442 at cam.ac.uk> wrote:
> Dear all
> I was going through the tutorial: http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate
> My question involves the first realignment and reslicing followed by second realignment and reslicing. I do not understand the step below:
> -> T = transform_vox2ctf/transform_vox2spm= transform_vox2ctf*inv(transform_vox2spm)
>   and this matrix is applied to sourcespace.
> What confuses me, is that
> a) we realign the anatomical voxel to spm (MNI) coordinates.
> b) we reslice and save it as shown in step "3. Preprocessing of the anatomical MRI: reslicing"
>                                       && 4. Preprocessing of the anatomical MRI: save to disk
> At this stage we get the transformation matrix anatomical voxel to spm i.e transform_vox2spm
> Moreover, we reside in the SPM coordinates now.
> c) We then realign to CTF coordinates, no reslicing is done. we Should
>  GET transform_spm2ctf. However, the obtained transform is called transform_vox2ct. Why???

Because the transformation matrix that is attached to the mri structure is always going from voxel space to a human interpretable coordinate system.

> We are using the resliced image mrirs= ft_volumereslice(cfg, mri_spm);
> c) During the source creation, we are already in the MNI coordinates, because we are using Subject01.mgz.

The fact that the file has the extension *.mgz does not mean that it is in MNI coordinates. The Subject01.mgz is created in the tutorial to have a transformation attached to it, that goes from (resliced) voxels to MNI.

> So, why in "STEP 4. Source model: Co-registration of the source space to the sensor-based head coordinate system we do we need to "
>         T = transform_vox2ctf/transform_vox2spm;
> Should it not be transform_vox2ctf changed to transform_spm2ctf
>  and T=transform_spm2ctf ???

No, it shouldn’t.


> best regards parham
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