SVReg Binaries and Modules

Overview

Surface-volume registration (SVReg) is an analysis sequence in part of the BrainSuite MR image analysis software.

This documentation will briefly describe the executables and files that are part of SVREG software. SVReg can be performed by using GUI interface. However, if you would like to become an advanced user for more specialized performance, this documentation can be helpful in both understanding how the software performs, how to deconstruct and utilize its separate components, set user specific parameters, and use optional flags.

SVREG consists of a series of modules that can either be called by using the main script through the command line (summarized in the flowchart shown right of the page), or through the BrainSuite GUI interface. This document first describes the main script and then describes the separate modules individually.

Before you begin

System Requirements
1. SVReg requires write permission to the working directory. Make sure to call your data from the appropriate directory.
2. SVReg reads, writes, and deletes data quickly. It is therefore recommended that your working directory is not in a syncing environment (such as dropbox). It is also not recommended to work from an external harddrive that may easily be disconnected unless you have a secure, high-speed peripheral connection.
3. SVReg requires ~4GB of physical memory to run successfully. SVReg will halt if memory runs out.
SVReg Directory
Your SVReg directory will be found in your BrainSuite directory indicated during installation. For most people this directory will be “C:\Program Files\BrainSuite16a1\svreg” where you’ll find a few subdirectories.
- Executable modules will be found in svreg’s subdirectory “bin”
  “C:\Program Files\BrainSuite16a1\svreg\bin”
- Two single subject atlas templates are provided:
SVReg Nomenclature
Only files with the indicated subbasename will be called during SVReg processing unless noted otherwise by appropriate flags. An error message will be shown if required file inputs are not found.

Modules Usage and Descriptions

svreg: The Main Script
Description:
Usage:
Example Usage:
Input files required:
Outputs
here
svreg_label_surf_hemi
Description:
Results:
Usage:
Example Usage:
Input files required:
Flags:
Outputs:
refine_ROIs2
Description:
Results:
Usage:
Example Usage:
Flags:
Input files required:
Outputs:
volmap_ball
Description:
Results:
Usage:
Example Usage:
Flags:
Input files required:
Outputs:
svreg_volreg
Description:
This is then followed by an intensity registration step using pvc.frac that refines the deformation map based on volumetric morphological features.
An intensity-based registration is performed to refine registration of non-cortical structures, including the subcotex, extra-cerebral structures, and hippocampus. This region is constrained by the boundary of the WM with addition of the brainstem and cerebellum dilated by 3 voxels.

Results:
Usage:
Example Usage:
Flags:
Input files required:
Outputs:
svreg_refinements
Description:
Results:
Usage:
Example Usage:
Flags:

Input files required:
Outputs:
refine_sulci_hemi
Description:
Results:
Usage:
Example Usage:
Flags:

Input files required:
Outputs:
generate_stats_xls
Description:
Results:
Usage:
Example Usage:
Flags:
Input files required:
Outputs:
clean_intermediate_files
Description:
Results:
Usage:
Example Usage:
Temporary folder subbasename.svreg.tmp is deleted:
thicknessPVC
Description:
Results:
Usage:
Example Usage:
Input files required:
Output files:
:
svreg_smooth_surf_function
Description:
Results:
Usage:
Example Usage:
Input files required:
svreg_make_atlas
Description:
Results:
Usage:
Input Files Required:
subbasename: File prefix of the subject that you want to convert into atlas.
atlasbasename: atlas from BrainSuite that was used to process this subject.
flag: -E means volumetric labels are manually edited.

Also see here.
svreg_apply_map
Description:
Results:
Usage:
Input Files Required:
map: This file contains a svreg map. (e.g. subbasename.svreg.map.nii.gz).
data: File containing the data to be warped
output: name of the output file
target: This file is used for getting dimensions and pixel resolution of the target image space.
generate_vol_param_stats_xls
Description:
Results:
Usage:
Input Files Required:
subject_fileprefix path and filename prefix of the subject’s output
from BrainSuite’s Cortical Surface Extraction
Sequence
param_nii_file File that contains scalar map
optional flags:
-v# Controls the verbosity of output messages (# is 0, 1, or 2)
-r Use if svreg sequence was run with refinement
svreg_resample
Description:
Results:
Usage:
Inputs:
in_file: input nifti file in nii.gz file format
out_file: output nifti file in nii.gz format
[dim]: if this is ‘-size’ output size is specified
if this is ‘-res’ output pixel resolution is specified
default is -res 1 1 1 (istotropic sampling)
[dx],[dy],[dz]: if the dim=’-size’, then this is interpreted as output size
if the dim=-res’, then this is interpred as voxel resolution in x,y,z directions
[method]: interpolation methods: ‘linear’, ‘nearest’,’cubic’,’spline’ the default is ‘linear’.
[extrapval]: Values for extrapolation outside the grid on the boundary.
svreg_smooth_vol_function
Description:
Results:
Usage:
Inputs:
in_file: input vol file
stdx,stdy,stdz: std dev (in mm) in 3 directions
out_vol: output vol file
svreg_get_mni_tal
Description:
Results:
Usage:
Inputs:
subbasename: subjects base name
atlasbasename: atlas base name
sx,sy,sz: xyz voxel coordinates
svreg_labelwith_atlas
Description:
Results:
Usage:
Inputs:
subbasename: subjects base name
atlasbasename: atlas base name
postfix: postfix to be appended to the output label files of the subject
svreg_sulcal_map
Description:
Results:
Usage:
Inputs:
subbasename: subjects base name
atlasbasename: atlas base name
XMLFile: XML file that contains atlas description
XMLSFile: XML file that contains description of sulcal anatomy
threshold: Threshold

SVReg Binaries and Modules

Overview

Before you begin

Modules Usage and Descriptions

Links

News