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open-discussion > RE: Changing default protocol before QC without GUI
Jul 29, 2020 10:07 PM | Martin Styner
RE: Changing default protocol before QC without GUI
Trying again, my first reply did not
post correctly. This time I will try to be more concise (maybe my
reply was too long):
1) -d should be used for generating & writing out a default protocol. It should NOT be used to run DTIPrep with a default protocol. DTIPrep investigate is the data to come up with thresholds for the default protocol and thus those thresholds are scan specific.
2) you should use the same protocol to run DTIPrep across a whole study. -d will run slightly different protocol (scan specific protocols), so do not use "-d" in that fashion
3) best use -d to generate a protocol, manually edit it (using DTIPrep's GUI) (e.g. to disable certain stages) and then save it for later use
4) then use -p to run it on the command line
Best
Martin
Originally posted by Steven Meisler:
1) -d should be used for generating & writing out a default protocol. It should NOT be used to run DTIPrep with a default protocol. DTIPrep investigate is the data to come up with thresholds for the default protocol and thus those thresholds are scan specific.
2) you should use the same protocol to run DTIPrep across a whole study. -d will run slightly different protocol (scan specific protocols), so do not use "-d" in that fashion
3) best use -d to generate a protocol, manually edit it (using DTIPrep's GUI) (e.g. to disable certain stages) and then save it for later use
4) then use -p to run it on the command line
Best
Martin
Originally posted by Steven Meisler:
Hi,
I am trying to run DTIPrep (1.2.10) in sbatch background jobs. For each subject, I use the -c and -d arguments to forego the need of any GUI, but I also now see that for my protocol, I should disable the eddy/motion correction and enable the dominant directional artifact check. Is there a way to have DTIPrep generate the default protocol without running QC, allowing me to edit it in command line, and then have QC run? I realize that I could make my own xml file for a study, but parameters such as IMAGE_directions vary between subjects.
I should note that I tried a line in the wiki which suggested to use only the -w -d and -p arguments to generate a protocol without running a check, but upon running, the GUI opened and nothing else happened.
Thanks,
Steven
I am trying to run DTIPrep (1.2.10) in sbatch background jobs. For each subject, I use the -c and -d arguments to forego the need of any GUI, but I also now see that for my protocol, I should disable the eddy/motion correction and enable the dominant directional artifact check. Is there a way to have DTIPrep generate the default protocol without running QC, allowing me to edit it in command line, and then have QC run? I realize that I could make my own xml file for a study, but parameters such as IMAGE_directions vary between subjects.
I should note that I tried a line in the wiki which suggested to use only the -w -d and -p arguments to generate a protocol without running a check, but upon running, the GUI opened and nothing else happened.
Thanks,
Steven
Threaded View
| Title | Author | Date |
|---|---|---|
| Steven Meisler | Jul 22, 2020 | |
| Martin Styner | Jul 29, 2020 | |
| Steven Meisler | Jul 30, 2020 | |
| Martin Styner | Jul 31, 2020 | |
| Steven Meisler | Aug 3, 2020 | |
| Martin Styner | Jul 27, 2020 | |
| Steven Meisler | Jul 29, 2020 | |