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

See also: HiResRecon
This page describes how to run the FreeSurfer recon-all for data with voxel sizes less than 1mm3 at native resolution. Several FreeSurfer binaries have been fixed to enable this feature. The pipeline is still under development, so please use with caution.
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See also: HiResRecon

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. Several FreeSurfer binaries have been fixed to enable this feature. The pipeline is still under development, so please use with caution.

Requred FreeSurfer 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 (we are working on it!), 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 need

1) a “-hires” flag or a "-cm" (both do the same thing)

2) an expert options file

Here is an example command line command:

recon-all -all -s $SUBJECT -hires -i $IMAGE -expert $EXPERT_FILE

Content of the expert options file

For more on expert options files see here.

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.

Running on launchpad

If you are running the submillimeter recon-all at the Martinos Center on launchpad, you might nead more than one node and 7GB of RAM. For 0.75mm3 voxels I have been using two nodes and 14GM RAM (and an -openmp flag to recon-all, e.g.)

pbsubmit -n 2 -c "recon-all -all -s $SUBJECT -hires -i $IMAGE -expert $EXPERT_FILE -openmp 2"

Data with 0.5mm3 resolution may need -n 8 or more, and take 3-4 days to finish, so be patient and good luck :) .

See also: HiResRecon

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