[Freesurfer] inter-hemisphere registration on customised template

2018-02-13 Thread Ting Qi
Dear Freesurfer experts,

I am writing to ask how to do the surface-based inter-hemispheric registration 
based on the customised template, instead of fsaverage. 

I am planning to calculate the lateralisation index for each vertex, which 
means I should to use the symmetry template, for example, fsaverage_sym. 
However, the current issue is my participants are children. Therefore it would 
be better to put the individual data to the customised average template, which 
is already created by ANTS in my case. So I was wondering how to perform the 
symmetry registration on this created template?

Thank you in advance. 

Cheers,
Ting 
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[Freesurfer] Coordinates in different modality and space

2017-02-13 Thread Ting Qi
Dear freesurfer experts,

I have some questions about the coordinates conversion, and the relationship 
between several types of coordinates. 

First of all, I’d like to confirm whether the coordinates reported in the 
results summary are based on MNI305 space? 

Second, I plan to combine multi-modalities data, therefore I would like to use 
the peak vertex in the surface as a seed to do additional volume-based 
analysis. I have the vertex index, vertex ras, MNI coordinates reported in the 
summary text, but how can I get the correct and corresponding volume 
coordinates in MNI space, particularly in MNI152? 

I read the page about the freesurfer coordinate system, they mentioned several 
cases about the transformation, but I still cant figure out what is the correct 
way in my case. Moreover, I tried the mni305 to mni152, but when I double 
checked the coordinates in mni152 space, the peak was no longer corresponds to 
the region reported in the mni305 space. So I sure there must be something 
wrong. 

Finally, would anyone offer me a explanation about the relationship between 
surface RAS, volume RAS, MNI* RAS, Vertex MNI, Volume MNI coordinates? It quite 
confused me.

Thanks in advance,

Best regards,
Ting







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