3D Tshift

  • Purpose: 3dTshift allows users to perform slice timing correction so that each slice that is acquired is

    aligned to the same temporal origin.

  • Usage: Below is an example of this command along with a definition of each subcommand. If you are interested

    in changing any of these parameters, you can type in "3dTshift -help" into the command line of any linux operating system that has afni installed. That will send a read out of all of the available options and a brief description about each one. To run the script below on a dataset, just enter it into an executable text file that is within your path, or in the directory you'll be running it from. Afni creator Bob Cox recommends performing slicetiming before other preprocessing steps, but the choice is up to you.

        3dTshift \
          -slice 5 \
          -prefix mydataset_slicetimed \
  • the "-slice 5" option tells the 3dTshift which slice number you want your slices to be aligned with temporally. Remember that afni starts counting from 0, so if you have 12 slices and want slice 6 to be used as the origin, you have to input it as slice 5.
  • the "-prefix mydataset_slicetimed" option allows you to specify the output name.
  • the last line with "mydataset+orig" is the dataset you want to use as your input.

NOTE: There are several other options you can use for this command, so I encourage you to check out the 3dTshift

help pages in linux