DIFFPREP phase and TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc does not exist

AFNI Message Board
1

Hi
1,if the phase was the LR and RL, should I choose the slice?
2,The registration settings file /home/zhangxiaochu/zharj/DIFF_PREP_WORK/TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc does not exist… Exiting
this is the script:

                        DIFFPREP                                               \
                             --dwi         $odir/LR.nii                         \
                                 --bvecs       $odir/LR_rvec.dat                    \
                                     --bvals       $odir/LR_bval.dat                    \
                                         --structural  $path_P_ss/anat_01/t2w.nii           \
                                             --phase       slice                             \
                                                 --will_be_drbuddied  1                             \
                                                     --reg_settings TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc

===
Thanks
rujing

2

Hi, Rujing-

While we do often use TORTOISE for DTI preprocessing with AFNI, TORTOISE-related questions should be directed to the TORTOISE software developers:
https://tortoise.nibib.nih.gov/

Re. your second question, this file:
TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc
would need to be created or downloaded (if you are following the instructions from the FATCAT preprocessing tutorial, it is downloaded as part of the TORTOISE Demo available from their website); that is just a default file of settings for running DIFFPREP; I don’t believe you need to use that file, but I usually start from one from the TORTOISE Demo used for the Bootcamp.

–pt

3

Hi Paul
Thanks for your reply. I will check that phase in Tortoise folks. Now I just remove option with the TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc , as I did not have this file. Then the program keep running. Did you mean that this option is not necessary for getting the fiber tracking?
Happy new year!
Rujing

4

Hi, Rujing-

It is really important to read the TORTOISE documentation before using the tool-- please see here:
https://tortoise.nibib.nih.gov/tortoise/v313

For a bit about what the *.dmc file is, see also the following paragraph from:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/Preprocessing_TORTOISE.html#diffprep
“For DIFFPREP itself, most of the inputs are fairly self-explanatory. Note that we flag that we will be following this processing with DR_BUDDI (via --will_be_drbuddied 1). We also note that the phase-encode direction was along the A-P axis of the volume (that is what --phase vertical signifies). Finally, we just use the default settings file from the TORTOISE folks (via --reg_settings *.dmc; note that this text file should be sitting in a directory with the following location and name: $HOME/DIFF_PREP_WORK/). For the AP data set, we then execute: …”
i.e., it is a registration settings file, setting parameters that you, the researcher, want. The one in the FATCAT Demo example comes from TORTOISE’s own Demo example-- it would be a good idea to check through it and make sure you know what the options are that are available, and what you want them to be (default or other).

–pt