Re: [Freesurfer] Resampling Question

Well, .3mm is still 30%, which means that your brains will show up 30% smaller/larger. This could mess up any number of things. Unfortunately, the right answer is to fix your data then re-run everything. Try using FreeSurfer's mri_convert to convert from dicom. You can also just pass the dicom directly to recon-all with the --i flag.

doug

Jeff Sadino wrote:

One more thing that might be useful: for my current dataset, everything was processed in FreeSurfer 4.3.1.

Thank you, Jeff

On Mon, Mar 7, 2011 at 12:41 PM, Jeff Sadino <jsadino.queens@gmail.com mailto:jsadino.queens@gmail.com> wrote:

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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