Removing dropped out directions in Tortoise 3?

Submitted by ceierud on Fri, 07/24/2020 - 15:02


Always thankful for your great software and upgrades!

In Tortoise calcvm 2.5.2 one could click  [display raw images] and delete a volume that had signal dropouts before completing DTI processing. Is it possible to do an analogous operation in Tortoise 3?

Best Regards,

Submitted by nayaka on Tue, 08/11/2020 - 08:20



In the new version, once you identify the volumes you are interested in eliminating from the set, the command to use will be ExtractDWISubsetListfile present in the DIFFPREP folder.

Example usage will be as follows:

If you identify vol 2, 3, 6 to be removed from a set of 64, the command will be provided as follows:

ExtractDWISubsetListfile  -i  <input.list>   -v  0-1, 4-5, 7-64

This will create  another listfile with corresponding NIFTI image and bmtxt file.

Please note: a visual inspection of bad volumes can be performed by examining the DWI nifti. If you have AFNI installed, you can also use the following command to compliment the process: 3dZipperZapper

This command will output a 1D (text) file containing a list of the bad volumes. You can use this text file as a guide to eliminate the volumes using ExtractDWISubsetListfile command. Very important component for the 3dZipperZapper to work is a mask that covers the whole volume of the brain that needs to be evaluated for artifacts.