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

[parham hashemzadeh]

Hi Jan
  Thank you.
best regards parham
On 2016-05-08 20:35, Schoffelen, J.M. (Jan Mathijs) wrote:
> 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,
> Jan-Mathijs
> 
> 
>> best regards parham
>> 
>> 
>> 
>> 
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> 
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-- 
best regards
Parham Hashemzadeh
Research Associate
Department of Applied Mathematics and Theoretical Physics
University of Cambridge, UK.
email: hashemzadeh at damtp.cam.ac.uk