Dear Team I tried to convert AFNI BRIK file to mgz using mri_convert. the MRI was shifted strangely. I overcame it by converting the MRI to nii using afni command (3dcopy) and from there to mgz with MRI convert. If you wish to fix the BRIK reader please see the info below.
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FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.2.0-51-generic x86_64
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shifted transformation matrix 0 0 -1 128.5 1 0 0 -127.5 0 -1 0 75.5
correct transformation matrix 0 0 -1 127 1 0 0 -127 0 -1 0 180
The MRI is aligned to a master supplied by brainhullhttp://kurage.nimh.nih.gov/meglab/Meg/Brainhullfor MEG position using the procedure described in the link. I can attach a BRIK file if anyone wants to dig into it. thanks Yuval
Dr .Harpaz
BIU MEG lab http://faculty.biu.ac.il/~goldsa/index.html