Caret:Operations/Freesurfer to fs LR

From Van Essen Lab

Revision as of 14:42, 19 June 2012

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 "Caret download page" for compatibility information.

Let SUBJECTS_DIR be the parent directory where multiple freesurfer-subject-directory subdirectories are located. (The script was written to be called from $SUBJECTS_DIR, but might work with an absolute path.)

Download freesurfer_to_fs_LR.v1.0.zip into/under $SUBJECTS_DIR.

unzip $SUBJECTS_DIR/freesurfer_to_fs_LR.v1.0.zip

cp $SUBJECTS_DIR/freesurfer_to_fs_LR/freesurfer_to_fs_LR.sh $SUBJECTS_DIR

Use a text editor to edit $SUBJECTS_DIR/freesurfer_to_fs_LR.sh to reflect your path locations:

CaretAtlasSpaceDirectory=$SUBJECTS_DIR/freesurfer_to_fs_LR/standard_mesh_atlases

Note: Replace $SUBJECTS_DIR with the actual pathname of the parent directory where your freesurfer-subject-directory subdirectories are located.

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

Run the script, e.g.:

freesurfer_to_fs_LR.sh bert

Example where $SUBJECTS_DIR=/mnt/myelin/donna/SAIS

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

/mnt/myelin/donna/SAIS/SAIS_001
/mnt/myelin/donna/SAIS/SAIS_002_MR1
/mnt/myelin/donna/SAIS/SAIS_003
/mnt/myelin/donna/SAIS/SAIS_004_MR1
/mnt/myelin/donna/SAIS/SAIS_009_MR1

The subdirectory 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
freesurfer_to_fs_LR.sh SAIS_002_MR1
freesurfer_to_fs_LR.sh SAIS_003
freesurfer_to_fs_LR.sh SAIS_004_MR1
freesurfer_to_fs_LR.sh SAIS_009_MR1

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

/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_001
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_002_MR1
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_003
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_004_MR1
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_009_MR1

Each of these subdirectories in /mnt/myelin/donna/SAIS/fs_LR_output_directory would have output files like those listed here.

The real magic of this script is in this command:

caret_command -surface-sphere-project-unproject \

   $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.sphere.reg.initial_mesh.coord.gii \

   $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.initial_mesh.topo.gii \

   $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.sphere.reg.reg_LR.initial_mesh.coord.gii \

   $OutputRootDir/$Subject/fsaverage/$Subject.$Hemisphere.sphere.164k_fs_"$Hemisphere".coord.gii\

   $OutputRootDir/$Subject/fsaverage/$Subject.$Hemisphere.def_sphere.164k_fs_"$Hemisphere".coord.gii \

   $OutputRootDir/$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 of 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 using a point projector to transform the vertices.

Repeat for the right. Vertex i on the left fs_LR 164k mesh should be in decent correspondence with vertex i on its right counterpart.