Dear Kristine,

I am currently experimenting with prepending to 
recon-all (of HCP pipelines 
) which does APCP alignment, robust FOV (cropping of unrelevant parts of image 
FOV - neck etc.), bias correction and (optionally) FNIRT-based skullstrip and 
gradient nonlinearity correction.

I believe that ACPC alignment could prevent Talairach registration 
errors/inaccuracies in recon-all which could have profound effect on subsequent 
skullstrip and subcortical labeling (it could at least prevent to disastrous 
errors which some other users reported recently, such as this: This 
could also help to mutual registration of data of multiple sessions (i.e. in 
longitudinal studies) to compensate different head positioning.

It  could be also beneficial to use FNIRT-based skullstrip to help (or even to 
replace) freesurfer's skullstrip (as is it done in of HCP 
pipelines), since, to my experience, the inaccurate skullstrip is basis of most 
errors in FreeSurfer reconstruction stream.
This FNIRT skullstrip works fine with our high-quality data from 64-channel 
coil acquired by protocol similar to Human connectome project (I ocasionally 
find only several, probably negligible amount of voxels of gray matter 
cut-out), but not as good with older data where significant parts of gray 
matter are often cut-out.

The drawback is that when you want to get to the original space, you have to 
account one more transformation and there is one more step in processing 
pipeline you need to check.

This is my view based on current experience. I would also greatly appreciate 
any comment (different perspective) of other users. 



Dear Freesurfer team,

This may sound like a bit of a small question, but I could not find any exact 
answer elsewhere.Does the exact orientation of the input image have much effect 
on the accuracy 
of the segmentation in Freesurfer?
It seems that some people apply ACPC alignment to the output of Freesurfer, so 
I am confused as to which order would be optimal.

Thank you in advance,

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