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

parham hashemzadeh ph442 at cam.ac.uk
Sun May 8 19:07:51 CEST 2016

Dear all
I was going through the tutorial: 
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= 
    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??? 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.
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 ???
best regards parham

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