Hello, I have a question about the effects of FreeSurfer's resampling algorithms. The way our pipeline goes is that we convert our DICOM images into .nii.gz format using FSL tools. One of the commands we use is FSLCPGEOM. I was never sure why, but our script would always break without it. Looking into it in more detail now, I see that it is replacing the voxel size information in the Nifti header with the voxel size in the template that FSLCPGEOM is copying from. This is causing all of our data to show isovolumetric 1x1x1 information in the header, even if the voxels really are non-isovolumetric. I have been having a difficult time combining FreeSurfer results across our different studies and I am wondering if this might be the reason why. All of our studies have voxels acquired near 1x1x1 isovolumetric, usually no more than .3mm away in any direction. What would the effect be of pushing data through the FreeSurfer reconstruction pipeline that is not really 1x1x1 isovolumetric?
Thank you, Jeff Sadino
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