Caret:Operations/Freesurfer to fs LR

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/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_009_MR1<br>
/mnt/myelin/donna/SAIS/fs_LR_output_directory/SAIS_009_MR1<br>
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Each of these subdirectories in /mnt/myelin/donna/SAIS/fs_LR_output_directory would have output files like those listed below.
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Each of these subdirectories in /mnt/myelin/donna/SAIS/fs_LR_output_directory would have output files like those listed below.[[Caret:Operations/Freesurfer to fs LR/Output]]
The real magic of this script is in this command:
The real magic of this script is in this command:

Revision as of 19:19, 19 March 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.

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
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
/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

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
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 below.Caret:Operations/Freesurfer to fs LR/Output

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 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.

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