3.2.1 Sample Registration Settings File

<!-- DTI data initialization file-->
<!-- do not remove the above comment line -->
<!--***************************************************************************-->
<!-- Effect. Specifies which undesirable effects will be corrected-->
<!-- rigid, rigid body motion correction-->
<!-- motion_distortion, rigid body motion and eddy current distortion correction-->
<effect>motion_distortion</effect>

<!--***************************************************************************-->
<!-- Perform motion and eddy distortion correction on DWI data.-->
<!-- on: perform motion and eddy distortion correction - HIGHLY RECOMMENDED-->
<!-- off: no registration will be done to align different DWI volumes to the-->
<!-- template image. Intended for quick testing purposes of the data only-->
<DWI_B0_registration>on</DWI_B0_registration>

<!--***************************************************************************-->
<!-- Smoothing prior to registration. Specify whether or not to smooth the-->
<!-- source and target images prior to registration (the final output-->
<!-- however, will not be smoothed). This is a good idea if performing the-->
<!-- correction with the 2D approach-->
<smoothing>off</smoothing>

<!--***************************************************************************-->
<!-- Smoothing algorithm. Will take effect only if <smoothing> is on-->
<!-- gaussian, gaussian-->
<!-- PM, Perona-Malik, gradient based anisotropic filtering-->
<!-- area, Perona-Malik, favoring large areas-->
<smoothing_algorithm>PM</smoothing_algorithm>

<!--***************************************************************************-->
<!-- gaussian_variance_text: Gaussian variance. Will take effect only if <smoothing> is on and-->
<!-- <smoothing_algorithm> is set to gaussian-->
<gaussian_variance>0.33330000</gaussian_variance>

<!--***************************************************************************-->
<!-- Kappa parameter. Will take effect if <smoothing> is on and the algorithm-->
<!-- is PM or area. Will also take effect if <automatic_kappa> is off-->
<kappa>35.000000</kappa>

<!--***************************************************************************-->
<!-- Automatically compute noise. Computes the mean and standard deviation for-->
<!-- both the structural and the template image-->
<!-- Syntax: on or off-->
<!-- If off noise values must be provided in the data description file-->
<automatic_noise_computation>on</automatic_noise_computation>

<!--***************************************************************************-->
<!-- Automatic kappa parameter. Determines the kappa value used for smoothing-->
<!-- during automatic noise computation-->
<!-- on, value is automatically determined - HIGHLY RECOMMENDED-->
<!-- off, the value specified in <kappa> will be used-->
<automatic_kappa>on</automatic_kappa>

<!--***************************************************************************-->
<!--Verbose level-->
<verbose>6</verbose>

<!--***************************************************************************-->
<!--Number of bins. Used to compute normalized mutual information-->
<nbins>48</nbins>

<<!--***************************************************************************-->
<!--Final diffusion weighted image output resolution (value in mm)-->
<img_resample_res>1.5000000,1.5000000,1.5000000</img_resample_res>

<!--***************************************************************************-->
<!--Final structural image output resolution (value in mm)-->
<structural_output_res>1.5000000,1.5000000,1.5000000</structural_output_res>

<!--***************************************************************************-->
<!-- Obtain bounding box based on FSL mask. Performs brain extraction with FSL s-->
<!-- bet tool and computes a bounding box for the brain to be used in the-->
<!-- registration process-->
<!-- on or off-->
<mask_fsl>on</mask_fsl>

<!--***************************************************************************-->
<!-- Rigid registration of structural to template image might fail even with-->
<!-- initial global search on. If that is the case, turn this tag on to use-->
<!-- ITKs registration pipeline instead of diff_prep to register the structural-->
<!-- image to the template-->
<!-- on or off-->
<ITK_structural_registration>on</ITK_structural_registration>

<!--***************************************************************************-->
<!-- Initial rigid body global search. Brings the template image into rough-->
<!-- alignment with the structural image. Recommended for data with large-->
<!-- rotational differences between the template and structural images-->
<!-- on or off-->
<initial_global_search>off</initial_global_search>

<!--***************************************************************************-->
<!-- Upsampling options-->
<!-- off: no upsampling-->
<!-- all: upsampling in all directions-->
<!-- slice_only: upsampling in slice direction only-->
<!-- b0_crop: does not do upsampling but does b0 extraction and cropping-->
<!-- If off than template image must be specified in data description file-->
<!-- If value entered does not match any of the above, it defaults to all-->
<upsampling>all</upsampling>

<!--***************************************************************************-->
<!--Upsampling factor-->
<upsampling_factor>2.0000000</upsampling_factor>

<!--***************************************************************************-->
<!-- Upsampling method. Determines the algorithm to use for upsampling-->
<!-- Will take effect only if <upsampling> is all or slice_only-->
<!-- nearest: nearest neighbor-->
<!-- linear-->
<!-- bicubic-->
<upsampling_method>bicubic</upsampling_method>

<!--***************************************************************************-->
<!--Scale diffusion intensity. Regular MRI and DTI signal intensities are on-->
<!--the order of 10^3 and this software works best in this range-->
<!--If the data in consideration has a different range, this "scale factor" can-->
<!--be used to scale the signal intensities by a constant during the upsampling-->
<!--Will take effect if <upsampling> is all or slice_only-->
<!--Integer values expected. Default value is 1 for no scaling-->
<scale_signal_factor>1</scale_signal_factor>

<!--***************************************************************************-->
<!--Desired FOV. Applied to template image during cropping (value in mm)-->
<cropped_FOV>200.00000,240.00000,190.00000</cropped_FOV_x>

<!--***************************************************************************-->
<!-- Perform EPI distortion correction with B-Spline registration. Steps 3 and 4-->
<!-- on or off-->
<bspline_EPI_correction>on</bspline_EPI_correction>

<!--***************************************************************************-->
<!--B-Spline grid resolution. Determines grid size of the B-Spline registration-->
<!--Will only take effect when <bspline_EPI_correction> is on-->
<!--Integer values generally ranging from 5 to 20 -->
<BS_EPI_parameters>5</BS_EPI_parameters>

<!--***************************************************************************-->
<!-- Activates the second order Eddy current transformations for-->
<!-- registering the B0 to the structural image -->
<!-- for better initialization of B-Splines registration-->
<eddy_correction_for_B0_to_structural>on</eddy_correction_for_B0_to_structural>

<!--***************************************************************************-->
<!-- Turns on the higher order registration terms for B=0 images.-->
<!-- Normally, these images should only require rigid terms to be registered to the first B0 volume-->
<!-- In case the data is a multi-series data with different scales for B=0 images-->
<!-- this can be turned on to correct for the scale/shear differences on B=0 images.-->
<eddy_correction_for_B0>on</eddy_correction_for_B0>

<!--***************************************************************************-->
<!-- The output structural and tempalte images will be in the chosen format-->
<!-- Either ANALYZE or NIFTI…-->
<image_format>NIFTI</image_format>

<!--***************************************************************************-->
<!-- Output Endianism. The desired endianism of the output images-->
<!-- big or little-->
<output_endianism>big</output_endianism>

<!--***************************************************************************-->
<!-- On to write the noise variance image computed through-->
<!-- many interpolation and transformation steps-->
<write_interpolated_variance>off</write_interpolated_variance>

<!--***************************************************************************-->
<!-- On : automatically compute the noise spatial correlation from the data-->
<!-- Off: Use the correlation matrix in Gustavo Rohde paper-->
<compute_corr_matrix>off</compute_corr_matrix>

<!--***************************************************************************-->
<!--Start at step. See FAQ for description of each step -->
<!-- 0, 3, 4, 5 -->
<start_at_step>0</start_at_step>

<!--***************************************************************************-->
<!--Stop at step. See FAQ for description of each step -->
<!-- 2, 3, 4, 5 -->
<stop_at_step>5</stop_at_step>

<!--***************************************************************************-->
<!-- Keep step 4 outputs.-->
<!-- on: keep files-->
<!-- off: delete files-->
<keep_step4_output>off</keep_step4_output>

<!--***************************************************************************-->
<!-- Keep ALL the intermediate, generated data.These include-->
<!-- Upsampled original data, Eddy & motion corrected data-->
<!-- on: keep files-->
<!-- off: delete files-->
<keep_intermediate_data>on</keep_intermediate_data>