DIFFPREP error messages

Submitted by Chris Panks on Thu, 05/09/2019 - 11:57


I get this error message right at the start of every run:

** Cannot find '@chauffeur_afni' from AFNI:
.: Event not found.
** Cannot find '@djunct_4d_imager' from AFNI:
.: Event not found.
Denoising DWIs for use in registration..

And this message at the very end of every run:

Writing final volume:   73
Starting QC...
** Cannot find '@chauffeur_afni' from AFNI:
.: Event not found.
Traceback (most recent call last):
  File "do_read_tort_transformations.py", line 77, in <module>
    tort_mot = read_tortoise_transformations(arg_list[0])
  File "do_read_tort_transformations.py", line 25, in read_tortoise_transformations
    fff = open( my_file ,'r')
IOError: [Errno 2] No such file or directory: 'TB0693U2_DWI/some/path/TB0693U2_DWI_merged_P_std_proc_eddy_transformations.txt'
1dplot: Command not found.
** Cannot find '@djunct_4d_imager' from AFNI:
.: Event not found.
Done.... Congratulations...

My assumption has been that these messages are shown because we don't use any of the methods described in the documentation under 'STEP 2: PREPARING AN ANATOMICAL IMAGE FOR EPI DISTORTION CORRECTION REORIENTATION OF FINAL IMAGE'.
Is my assumption correct? Or do I need to do something with regard to these messages?

Thank you,


Chris Panks


Submitted by nayaka on Tue, 05/21/2019 - 18:15


Hi Chris,

This is an error message that comes up during TORTOISE processing as the default assumption is that AFNI software has been installed on your computer. Since the option --do_qc is switched on by default during processing, if AFNI is not present you will get these errors. These error messages will not affect your final processing results nor are they related to the step 2:preparing anatomical image for epi distortion correction 

The AFNI commands incorporated are related to the generation of files as shown in step8: DIFFPREP input output quality check. The png and gif files generated during processing (DIFFPREP/DRBUDDI) can be examined for quality of data before and after correction. This is now conveniently stored in a QC folder within the proc folder. If would like to use these QC features, we recommend installing AFNI on your machine. 

Please note: While it is convenient to get these QC images generated during processing, if you are not interested in generation of these files, you can just provide the tag --do_qc 0 in your processing command and it will bypass the QC step.