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3.2.17 Initial Upsampling

<upsampling></upsampling>

  • off
  • on Default Setting
  • slice_only
  • b0_crop

The users are given the option to upsample the DW images, including B0, by a desired factor before starting the registration process. The default value is all, which will upsample the images as well as perform some other critical operations, as described below.

Note that upsampling is only performed internally before registration in order to improve the quality of the registration results. Only a single interpolation step is performed on the raw data, using a combination of all transformations calculated in the software. See the pipeline diagram for more details.

If you are working with data smaller than 256x256, we highly recommend the use of upsampling in this software. However, if your data is 256x256 or higher we recommend not upsampling due to disk space and memory limitations. In this case, use the b0_crop option.

Description of each option:

  • off: No upsampling is done and the template image is not created. If this option is chosen, the user needs to define the full path to the template file in the data description file.
  • all: The default value. The images are upsampled in all directions (x,y,z). For example an image of size (128x128x100) will be upsampled to (256x256x200) if the upsampling factor is 2. Please also note that a NEW dataset is created with the new resolution, including the listfile, B-matrix and path files.
  • slice_only: The images are upsampled only in slice direction (z). For example an image of size (128x128x100) will be upsampled to (128x128x200) with upsampling factor 2. Like in the previous case, a new data set is created if this option is chosen.
  • b0_crop: No upsampling is performed but the B0 image is automatically extracted from the DWI set, and then cropped to fit the desired FOV and saved as an ANALYZE or NIFTI image to be used as the template image. This is the recommended setting for high resolution data, and for data that has been zero filled at the scanner.