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3.1.2 Data Description File

To run the program, the user needs an additional file describing the data, called the data description file. This XML file contains all the necessary information about the data to run the software. A sample data description file is displayed on the next page.

For manual creation of the data description file for use with the command line version of DIFF_PREP, the user needs to replace the values in between the tags with the information based on their data. The mandatory tags in the file are:

PROCBASE

This tag defines the full path to the main folder which contains the listfile, the path file and the Bmatrix file. Most intermediate and final output files of the software are going to be placed in this folder.

Example:

<PROCBASE>/home/main_data_folder/specific_data_folder/</PROCBASE>

The user should replace the path in between <PROCBASE></PROCBASE> to the correct path.

list_root_filename

This tag defines the name of the listfile to be used. Please note that it is just the filename and not the full path and that it is assumed that this file exists in the PROCBASE folder.

Example:

<list_root_filename>sample.list</list_root_filename>

STRUCTURAL_FILENAME

This tag defines the full path to the structural image file. The file should be in analyze or nifti format and the path should point to the ".nii" or ".img" (not the ".hdr" file). Note that this is an optional image to provide. If none is provided, the 1st b0 image in your DTI dataset will be extracted and used as a target. In this case, the user should set the 'Correction for B0 distortion with BSplines' to off, as a non-epi image is required for this correction.

Example:

<STRUCTURAL_FILENAME>/home/main_data_folder/specific_data_folder/structural.img</STRUCTURAL_FILENAME>

registration_filename

This tag defines the name of the registration settings file. The details of this file will be explained in Section Registration Settings. Please again note that this is not the full path but just the filename and this file must be located in the DIFF_PREP_WORK directory in the user's home directory, with the extension .dmc. If that is not the case, the program will display an error message.

is_brain_data

The software behaves differently if the data to be used is brain data or phantom data. This tag indicates the type of the data. It can be "yes/no". Note that if your images do not have roughly whole brain coverage, it is necessary to select "no". By default, this is set to yes (the radio button of the GUI is automatically selected when you first load the software).

Example:

<is_brain_data>yes</is_brain_data>

The following tags are optional:

TEMPLATE_FILENAME

This tag defines the full path to the template image to be used in the registration. If it is provided, the value in this tag will be used. Otherwise, a template image will be automatically created from the b0 image in the DTI data set. The automatic b0 template creation is the recommended procedure.

REORIENTATION_FILENAME

This tag defines the full path to an optional template for final reorientation. This can be used if a different target than STRUCTURAL_FILENAME is desired for the final reorientation of the data. An example of a target could be the ICBM atlases, or other atlas type images.

upsample_name

Currently, this is referred to in the software as "anonymize name". If a name is specified here, a copy of the original data will be made with the specified name, and all processing will be performed with the new name. This is intended as a means of anonymizing data. This functionality used to be associated with the upsampling procedure, but has been replaced with an independent re-naming function (as of V1.0.1).

Example:

<upsample_name>subject_57_up</upsample_name>

The following tags are needed ONLY WHEN the "automatic_B0_noise" setting is turned off in the registration settings file. Otherwise, they are not needed. The default value is 0.0 as a place holder only. If "automatic_B0_noise" is set to off, please supply appropriate values.

B0_noise_mean

This tag defines the mean intensity value of the background in the b0 image.

Example:

<B0_noise_mean>0.0</B0_noise_mean>

B0_noise_stdev

This tag defines the standard deviation of the noise in the background of the b0 image.

Example:

<B0_noise_stdev>0.0</B0_noise_stdev>

structural_noise_mean

This tag defines the mean of the noise in the background of the structural image.

structural_noise_stdev

This tag defines the standard deviation of the noise in the background of the structural image.

display images and log

Un-checking this check box will make sure the image registration window is not displayed when running batch processing from command line.