Submitted by Ashika on Fri, 05/07/2021 - 04:26

Dear experts,

I ran DIFFPREP command to perform distortion correction using structural data. I used --step 0, assuming that all three corrections would be performed. But in the final image I expected to see an output file  with generic name _EPI_field.nii. I got an output(the name that I specified in -o flag) .nii. Does this mean that epi distortion has been done?


 --step 0: Big bang. The start of everything...
            1: Motion & eddy currents distortion correction. Initial image creation steps are assumed to have been done and that the files are present.
            2: EPI distortion correction. Motion and eddy transformation files are assumed to be present.
            3: Final resampling and reorientation.
          Start step. You can continue a previously interrupted run with this option.



Secondly, Is registration setting required for human data? Can we use example_registration_settings.dmc or TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc.

Or do we have to modify its contents according to fov parameters of T2w image?



Thank you in advance

Submitted by nayaka on Tue, 05/11/2021 - 10:38


Hi Ashika,

1) Yes, the output data is EPI distortion corrected. If you do not want it performed, you can override the settings file by providing a specific tag in DIFFPREP command line i.e  --epi off

You can check the settings file but default in the last release was to perform EPI correction unless otherwise specified. 

2) You do not have to provide a settings file for human data and can override the default by specifying tags in command line: 

 example: the settings file has output resolution of 1.5 mm isotropic. If you want specific output resolution, you can provide the --res tag with the desired resolution.