View source

Data that have been processed by standard Freesurfer ‘recon-all’ (tested with v5.1, but may work on older versions) can be converted to the 164k_fs_LR mesh using this ‘freesurfer_to_fs_LR’ script.  NB:  This is a BETA version, so please be patient, and email [donna@brainvis.wustl.edu] if technical problems arise.

This script is a streamlined version of Matt Glasser's FreeSurfer2CaretConvertAndRegisterNonlinear.sh script (currently under development for the Human Connectome Project).  Several steps were removed:  nonlinear spatial normalization (replaced with affine talairach.xfm); brain mask; downsampling; and caret workbench stuff.

This script is used like so:

	freesurfer_to_fs_LR.sh freesurfer-subject-directory

You must have both freesurfer (tested on 5.1, but may work on older versions) and Caret v 5.64 or higher installed for the script to work, as it calls command line utilities in those distributions (e.g., mri_convert, mri_info, caret_command).  See [http://brainvis.wustl.edu/wiki/index.php/Caret:Download "Caret download page"] for compatibility information.

It was written to be called from within the same directory where freesurfer-subject-directory is located, but might work with an absolute path.

Before running freesurfer_to_fs_LR.sh, be sure to edit this variable location appropriately:

	CaretAtlasSpaceDirectory=/mnt/myelin/donna/ATLAS/fs_LR/standard_mesh_atlases<br>
	Note:  The standard_mesh_atlases subdirectory is included with this zip file, so point this to where you unpacked it.

Check your Freesurfer installation path, too:

	FreeSurferInstallationDirectory=/usr/local/freesurfer

If you don't like this name for the output subdirectory, change it:

	OutputRootDir=fs_LR_output_directory

Save your edits; chmod +x freesurfer_to_fs_LR.sh, if needed; and run the script, e.g.:

	freesurfer_to_fs_LR.sh bert

Note that this command was written to be run in a directory like this:

/mnt/myelin/donna/SAIS

... which has several Freesurfer subject directories under it, e.g.:

/mnt/myelin/donna/SAIS/SAIS_001<br>
/mnt/myelin/donna/SAIS/SAIS_002_MR1<br>
/mnt/myelin/donna/SAIS/SAIS_003<br>
/mnt/myelin/donna/SAIS/SAIS_004_MR1<br>
/mnt/myelin/donna/SAIS/SAIS_009_MR1<br>

In other words, it might be your Freesurfer $SUBJECTS_DIR directory.  One of these is your input to this command; its contents are read, but not modified (e.g., ?h.white, ?h.pial, ?h.sphere, ?h.sphere.reg, ?h.curv, ?h.sulc, ?h.thickness, orig.mgz, talairach.xfm).  Outputs go to $OutputRootDir.

If OutputRootDir=fs_LR_output_directory and you run this command once for each of subject directory, e.g.:

freesurfer_to_fs_LR.sh SAIS_001<br>
freesurfer_to_fs_LR.sh SAIS_002_MR1<br>
freesurfer_to_fs_LR.sh SAIS_003<br>
freesurfer_to_fs_LR.sh SAIS_004_MR1<br>
freesurfer_to_fs_LR.sh SAIS_009_MR1<br>

... then you would get output subdirectories like this:

/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_001<br>
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_002_MR1<br>
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_003<br>
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_004_MR1<br>
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_009_MR1<br>

Each of these subdirectories in /mnt/myelin/donna/SAIS/fs_LR_output_directory would have output files like those listed [[Caret:Operations/Freesurfer_to_fs_LR/Output here]] [Caret:Operations/Freesurfer_to_fs_LR/Output "here"].

The real magic of this script is in this command:

  caret_command -surface-sphere-project-unproject \<br>
    $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.sphere.reg.initial_mesh.coord.gii \<br>
    $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.initial_mesh.topo.gii \<br>
    $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.sphere.reg.reg_LR.initial_mesh.coord.gii \<br>
    $OutputRootDir/$Subject/fsaverage/$Subject.$Hemisphere.sphere.164k_fs_"$Hemisphere".coord.gii\<br>
    $OutputRootDir/$Subject/fsaverage/$Subject.$Hemisphere.def_sphere.164k_fs_"$Hemisphere".coord.gii \<br>
    $OutputRootDir/$Subject/fsaverage/$Subject.$Hemisphere.164k_fs_"$Hemisphere".topo.gii

Its usage is like so:

      caret_command -surface-sphere-project-unproject  
         1<input-spherical-coordinate-file-name>
         2<input-spherical-topology-file-name>
         3<output-spherical-coordinate-file-name>
         4<project-to-spherical-coordinate-file-name>
         5<unproject-to-spherical-coordinate-file-name>
         6<project-unproject-spherical-topology-file-name>
         
         Transform a spherical surface.
         
         The input spherical surface is projected to the 
         "project-to" surface using barycentric projections
         and then unprojected using the "unproject-to" 
         spherical surface.  Typically the "unproject-to"
         surface is created during surface-based registration
         of the "project-to" spherical surface to some
         target.

Pseudocode for left hemisphere:

1.  Project SAIS_001/surf/lh.sphere.reg to $FreeSurferInstallationDirectory/subjects/fsaverage/surf/lh.sphere.reg.  (Because we're using sphere.reg, they should be in good geographic agreement, so this is a more or a resampling from initial mesh to the Freesurfer hemisphere-specific 164k mesh.)

2.  Unproject the hem-specific 164k sphere onto the hemisphere-independent (fs_LR) sphere.  This keeps the nodes the same, so there is no resampling, but the geography gets swapped around, so that node i in both left and right is in decent correspondence.  (In the hem-specific spheres, node i might be in the frontal lobe on the left, occipital on the right.)  [DVE: I'm not sure this is technically correct - see email]

Repeat for the right.