NIHDMCS_V2

This document outlines the steps needed for upgrading to the newest version of the NIHDMC software.

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_v2'

2. 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_v2

3. The name of the final output of the software has been shortened. The old naming system of ..._rpd_final_results.list has been replaced with ..._DMC.list. For more information on the naming convention, please see the FAQ.
4. In order to help keep track of what is being done to the data, 2 tags have been added to the list file. They are:

<!-- Upsampling method used -->
<upsampling></upsampling>

<!-- EPI Correction Method -->
<EPI_correction_method></EPI_correction_method></pre>

These 2 tags will tell you what type of upsampling you used (all, slice only, etc) and what type of EPI correction (NO_EPI, B-Spline (BSP), etc.)

5. The registration settings file has been changed dramatically. Please note that your existing registration settings files will not function properly with this version as a number of variable names have been changed! The changes are listed below.
1. The upsampling options have changed so that the old option 'none' is now called 'b0_crop'. This is to differentiate it from the option 'off', and reflects that while it does not do any upsampling, it still extracts and crops the b0 image. The new tag looks like:

<!--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-->
<upsampling>b0_crop</upsampling>

2. The following tag has been removed. By default now the template image will always be saved.

<!-- save the reference image as a template image?-->
<save_template>on</save_template>

3. The following variable has been renamed:

<automatic_B0_noise>on</automatic_B0_noise>

It has been changed to the following to reflect that it computes noise for both the b0 image and the structural image. The functionality has not changed.

<automatic_noise_computation>on</automatic_noise_computation>

4. The following variable has been renamed:

<automatic_B0_kappa>on</automatic_B0_kappa>

It has been renamed to the following:

<automatic_kappa>on</automatic_kappa>

5. Important Change to Functionality: In the case where the initial rigid body registration of the structural to the template image fails, we have added an alternative ITK based rigid body registration algorithm, controlled by the following tag. Note that if this is set to 'on', the NIHDMC built in rigid body registration algorithm is not used, and the 'initial_global_search' cannot be used. If it is set to 'off' than everything will run as before, and you have the option to use 'initial_global_search' if you like.

<!--***************************************************************************-->
<!--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 -->
<!--ITK's registration pipeline instead of NIHDMC to register the structural-->
<!--image to the template-->
<!--'on' or 'off' -->
<ITK_structural_registration>off</ITK_structural_registration>

6. Important Change to Functionality: The old tag for controlling the B-Spline factor allowed for the entry of 2 different numbers.

<!-- BS_EPI parameters-->
<BS_EPI_parameters>7,3</BS_EPI_parameters>

However, we have found that the 2^nd number should always be 3. Therefore, it has been hard coded, and you must now enter only 1 number.

<!-- BS_EPI parameters-->
<BS_EPI_parameters>7</BS_EPI_parameters>

The above example of the old and new versions would result in an identical B-Spline registration.

7. Important Change to Functionality: The old system of "skip" versus "keep" was rather confusing and in that regard, the following 2 tags have been changed:

<!-- Skip B-Spline Registration (Step 3 and 4)-->
<skip_bspline>off</skip_bspline>

&hellipis now the much more logical system of 'on'=do the B-Spline, and 'off'=do not do the B-Spline.

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

Similarly…

<!--Skip motion/distortion correction?-->
<skip_mdc>off</skip_mdc>

…is now:

<!--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>

8. The following tag has been removed.

<!-- Write brain mask as an output Analyze file?-->
<write_fsl_output>off</write_fsl_output>

6. New GUI implementation!! For ease of use, we have implemented a GUI. You will still need to create/edit your registration settings file as before, but the data description file is automatically created for you in this GUI. For detailed description of the GUI please click here.