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The method works well for voxel sizes 0.75 mm3. It should work with voxel between 1mm3 and 0.75mm3. It DOES NOT work with 0.5 mm3 voxels or below, and It has not been tested with anisotropic voxels. The method works well for voxel sizes 0.75 mm3. It should work with voxel between 1mm3 and 0.75mm3. Inputs with 0.5 mm3 voxels or below will have a brainmask failure, but if you fix the brainmask manually, the rest of recon-all should work well. We haven't tested the stream for inputs with anisotropic voxels.
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Your expert options file should contain the number of iterations for surface inflation that is more than the FreeSurfer’s default (10). The number of iterations depends on image resolution. For the 0.75mm isotropic voxels we found the necessary n iterations to be 15, i.e. your expert options file will contain:mris_inflate -n 15
More inflation is necessary for correct surface mapping onto a sphere and subsequent defect labelling. In the future we hope to have FreeSurfer determine the number of iterations automatically depending on the image resolution, but for now the expert options file works fine.
Your expert options file should contain the number of iterations for surface inflation that is more than the FreeSurfer’s default (10). The number of iterations depends on image resolution. For the 0.75mm isotropic voxels we found the necessary n iterations to be 15, i.e. your expert options file will contain:mris_inflate -n 15 More inflation is necessary for correct surface mapping onto a sphere and subsequent defect labelling. In the future we hope to have FreeSurfer determine the number of iterations automatically depending on the image resolution, but for now the expert options file works fine.

Recon with native submillimeter resolution

This page describes how to run the FreeSurfer recon-all for data with voxel sizes less than 1mm3 at native resolution.

Requred version

dev version built after August 2015 or FreeSurfer 6

Note on the voxel size

The method works well for voxel sizes 0.75 mm3. It should work with voxel between 1mm3 and 0.75mm3. Inputs with 0.5 mm3 voxels or below will have a brainmask failure, but if you fix the brainmask manually, the rest of recon-all should work well. We haven't tested the stream for inputs with anisotropic voxels.

How-to

To run all of the recon-all pipeline at native resolution, you need1) a “-hires” flag2) an expert options fileHere is an example command line command:recon-all -all -s $SUBJECT -hires -i $IMAGE -expert $EXPERT_FILE

Content of the expert options file

Your expert options file should contain the number of iterations for surface inflation that is more than the FreeSurfer’s default (10). The number of iterations depends on image resolution. For the 0.75mm isotropic voxels we found the necessary n iterations to be 15, i.e. your expert options file will contain:mris_inflate -n 15 More inflation is necessary for correct surface mapping onto a sphere and subsequent defect labelling. In the future we hope to have FreeSurfer determine the number of iterations automatically depending on the image resolution, but for now the expert options file works fine.

SubmillimeterRecon (last edited 2017-10-28 16:07:43 by NataliaZaretskaya)