Hello, some of my MRIs do not seem to be aligned. So I used ACPCdetect to realign on my acpc. The problem is that it works well on the NIFTI but the recon-all freesurfer procedure seems to return it to me at the starting point. Is this kind of alignment problematic in brainstorm?
(left side are nifti my aligned file and right is my freesurfer output file (recon-all -i = my aligned nifti file .nii)Thank again!
Hello,
By default, FreeSurfer rewrites the input volume following its own standard (256x256x256 volume, 1mm3 voxels). So it is normal if your observe differences between the input and output volumes.
The orientation of the volume doesn’t matter. What is important is the correct position of the NAS/LPA/RPA points, and optionally the correct MNI affine transformation.
http://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Automatic_registration
http://neuroimage.usc.edu/brainstorm/CoordinateSystems
Francois
Awesome! Thank you verry verry much again!
Have a good day
