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NIHDMCS_V2.1

Please follow the following steps to update to the newest version of the 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_v2.1'
  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_v2.1

Important!

There are major changes to this version of the software. Please read all of the following to ensure you understand the differences. If you have concerns, please contact us.

  1. In previous versions of this software, the data was interpolated up to 4 times: upsampling, motion and eddy correction (as one interpolation step), epi correction, and final reorientation. In this version, all transformations have been combined into a single interpolation step. This should reduce errors introduced by interpolation. This does not change the way in which the software is used.
  2. The software can now output noise variance images. These are used by the NIHDTI software as noise variance values in the chisq formulation of the tensor fitting function. The noise values are a voxelwise varying function, as opposed to the single value noise variance used in the past. This function is still in beta testing, and as such we have set the default to not save these images. If you attempt to use this function, please report any error messages you may encounter. Be aware that it is likely you will encounter errors, and we strongly recommend setting these tags to the default value of 'off'.
  3. The registration settings file has changed slightly. Two new tags have been added to facilitate the noise variance images. The default value for both tags is off, as they are still in beta testing. The new tags are:
<!--***************************************************************************-->
<!-- 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>
  1. The tag <write_extra_files> is now set to on by default. This file is required for the calculation of the noise variance images. If you create your registration settings file by the GUI (see section 3.1.4 of the software guide for more information) than this option is grayed out so that it cannot be changed. You can still edit this manually in your text file if you desire to have it set to off. Note that this only writes a small number of text files and does not appreciably add any time to the pipeline. Therefore, we recommend that this option be set to on.
  2. A small bug in the cropping of the b0 images was fixed, and the cropping algorithm was made more robust.