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Dear,

As part of our invasive work, we would like to extract the mni coordinates of intracranial electrodes. To this end, we follow the following procedure:

1) Pre-implant MRI and Post-implant CT are coregistered using SPM. 2) The pre-implant MRI is processed using the recon-all function. 3) The CT is conformed to the 256^3 space, using 'mri_convert ct.nii ctConformed.nii --conform --nochange' 4) The coordinates (in mri-space, i.e. row-column-slice) of the intracranial electrodes are extracted using a custom semi-automated Matlab script. 5) When recon-all finished, the subject is being warped to MNI space, using 'mri_cvs_register --mov subjectId --mni'

The last step returns the non-linear warp in an m3z-file. I now want to apply this transformation to the coordinates of the electrodes. For this, I load the m3z-file in matlab, using the 'mris_read_m3z.m' provided by the freesurfer development repository, which gives me two 4-dimensional matrices (256 x 256 x 256 x 3): vol-orig and vol-dest. However, I cannot find any documentation how to interpret these matrices. Could you provide any information on how I would interpret these matrices, and how to apply the warp to the list of CT coordinates (in row-column-slice) to obtain their mni coordinates?

Thank you in advance.

Best regards, Benjamin Wittevrongel Laboratory for Neuro- and Psychophysiology KU Leuven