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NIHDMCS_04_25_2008

This document outlines the steps needed for upgrading to the newest version of the NIHDMC software. Note that small changes have been made to both the registration settings file and the data description file.

  1. Open ~/.aliases in a text editor. Add the following line, or if this alias already exists, please edit it to match the following:
alias nihdmcs 'cd /raid3/STBBapps/NIH_DMC_source_04_25_2008'
  1. Once this alias has been updated, open a new terminal and type nihdmcs. Make sure that your present working directory is correct.
pwd
/raid3/STBBapps/NIH_DMC_source_04_25_2008
  1. Make sure that you have the following directory: ~/NIH_DTI_WORK.
  2. In the new source directory, there are 2 new files: sample_registration_settings.xml and sample_data_description.xml. These are the new sample files to use as your template for creating your own data description and registration settings files. Copy the sample_registration_settings.xml file to ~/NIH_DTI_WORK. All registration settings files are now stored in that directory so as to avoid permissions issues with having them stored in the source code directory. As before, this file can have any name, and you can have multiple registration settings files. The name of the registration settings file that you wish to use is still specified in the data description file.
  3. The new data description file has only one change. There is now a tag that looks like this:
<!-- Structural Image's Modality..... T1 or T2 or PD-->
<STRUCTURAL_MODALITY>T1</STRUCTURAL_MODALITY>

The default value is T1.

  1. The registration settings file has been simplified to remove old (unsupported) options, as well as to add some new functionality. New tags include:
<!-- final output resolution-->
<img_resample_res>1.5,1.5,1.5</img_resample_res>

This tag controls the final output resolution (in mm) of your diffusion data. The default value is 1.5mm isotropic.

<!-- new resolution for structural image output-->
<structural_output_res>1.5,1.5,1.5</structural_output_res>

This tag defines the final output resolution of the structural image that you define in the data description file. Default value is 1.5mm isotropic (same as the img_resample_res).

<!-- upsampling method... "Nearest" or "bicubic" - only works for upsampling=all-->
<upsampling_method>nearest</upsampling_method>

This defines the interpolation method used for the initial upsampling step. Previously this was hard coded to Nearest Neighbor. This is largely untested to date. The default value is nearest to maintain the same upsampling as the old version of the code.

Summary

  • Make sure that the registration settings file you wish to use exists in ~/NIH_DTI_WORK. The code will crash otherwise. You will need to make a new registration settings file, as the old ones you were using will no longer have the correct tags.
  • The new source code directory is /raid3/STBBapps/NIH_DMC_source_04_25_2008
  • The old source code directory, including your old registration settings files are still available at /raid3/STBBapps/NIH_DMC_source