open-discussion > Create XML file without running checking
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Dec 2, 2015  06:12 AM | Jian Zhang
Create XML file without running checking
Hi experts,

We want to use the command line of DTIPrep to create XML file and then modify it, using the command as below:
DTIPrep -d -p SomeProto.xml -w dwi.nrrd
But, only the GUI of DTIPrep will be launched, so we set the command like this:
DTIPrep -d -c -p SomeProto.xml -w dwi.nrrd
We got the default protocol file, but this command run the whole quality check procedure!
Can you help us to point out how to create the default protocol XML file via command, without running the whole quality check, so that we can quickly modify XML file and then run the next command:
DTIPrep -c -p Modified.xml -w dwi.nrrd
OR is there any way to combine these 2 steps together?

Thank you very much!

-Jian
Dec 4, 2015  10:12 AM | Martin Styner
RE: Create XML file without running checking
Hi Jian
Sorry for the delay in answering. 
1. the way to run DTIPrep is to use the same protocol within a given study. You do not want to have different protocol files in the same study, as this could significantly bias your analytical results. So, only run the command to create the default protocol only once.

2. while the default protocol is okay, it is worthwhile to change it to your needs (e.g. if you have sedated scans, you may want to turn off the motion correction). Thus, I suggest you start up the GUI of DTIPrep and use its interface to generate the default protocol, adapt it and then save it for future use in the command line executions.

3. Finally, you are right, there is currently not a way to create the default protocol only on the command line mode. Something to correct for future uses, can you create a feature request on the github/source code issue tracker?

Thanks
Martin
Dec 5, 2015  04:12 AM | Jian Zhang
RE: Create XML file without running checking
Hi Martin,

Thanks for your answer.

1. The reason for us to create protocol for every participant is that the b vector values are different during participants, even thought they are scanned under the same protocol, we want to extract the gradient information into the XML file for everyone, without changing other option. If we use the public protocol for all participants, the gradient information would be the first one, not the real value of others. Do you think we can accept this little difference and ignore it?

2. Besides the command line way to create the default protocol, can you add other options for command line mode (e.g. turn off the motion correction) in future.

3. I have create the feature request on the github/source code issue tracker.

Thanks
-Jian
Dec 6, 2015  10:12 AM | Martin Styner
RE: Create XML file without running checking
Re 1) if b-values (or b-vectors) are different across subjects, I hope you do NOT plan to use them in the same study, as such a study would not be appropriate, diffusion based properties (such as FA or GFA), are far to sensitive to changes in those.

If you have (e.g. for purpose of testing) different b-vectors or values, and don't want DTIPrep to test for that, simply disable the diffusion information check in the protocol file. 

In general, I think there is a misconception how DTIPrep operates. One should not change parameters etc on the command line, but rather create protocol files where all parameters (and there are many) can be adapted to the given study. It is simple to enable/disable motion correction in the protocol files, and that's the place where it should be modified (not on the command line).
Dec 7, 2015  08:12 AM | Jian Zhang
RE: Create XML file without running checking
Thanks, I get it.
Dec 11, 2017  08:12 AM | Michael Dayan
RE: Create XML file without running checking
Hi,

Just as a follow up. It is actually not uncommon for the gradient directions to be encoded according to the patient position rather than the scanner coordinate system. As such there is nothing wrong in having a different set of diffusion gradient coordinates for each subject (they are simply rotated according to the patient position, with same number of directions and same b-values).

In this case, would it be possible to know how to change the protocol file on the command line? Or is it still not an option?

Thank you,

Michael
Dec 11, 2017  10:12 AM | Martin Styner
RE: Create XML file without running checking
The QC procedure/protocol (stored in XML format) does not need to check the gradient directions. Just turn off that step and it does not matter what directions are in the protocol.

Best
Martin
Jan 3, 2018  03:01 PM | Rachel Steiner - University of Wisconsin - Madison
RE: Create XML file without running checking
Hi Jian,

Load a representative raw dwi dataset from your study in the GUI, go to the protocol tab, click default protocol, then click “save as” to save the xml file somewhere before clicking “Run.” You can modify the default parameters right there in the GUI then save it again as the new modified xml without running the whole processing. Just click save rather Jan run protocol.

Alternatively, run a new dtiprep window to open up that default xml file younjust saved and manually modify using the GUI and then save as a different name somewhere safely to be used on the command line ... on the command line you will be pointing the -p to the absolute path where you’ve saved the modified xml. For example, /Home/safe/modified. xml

Did I understand your question correctly? Are you having an issue finding a save as button in the GUI window with your version of dtiprep?

Rachel



color=#000000]
[/color]Originally posted by Jian Zhang:
Hi experts,

We want to use the command line of DTIPrep to create XML file and then modify it, using the command as below:
DTIPrep -d -p SomeProto.xml -w dwi.nrrd
But, only the GUI of DTIPrep will be launched, so we set the command like this:
DTIPrep -d -c -p SomeProto.xml -w dwi.nrrd
We got the default protocol file, but this command run the whole quality check procedure!
Can you help us to point out how to create the default protocol XML file via command, without running the whole quality check, so that we can quickly modify XML file and then run the next command:
DTIPrep -c -p Modified.xml -w dwi.nrrd
OR is there any way to combine these 2 steps together?

Thank you very much!

-Jian
Jan 3, 2018  03:01 PM | Rachel Steiner - University of Wisconsin - Madison
RE: Create XML file without running checking
Oops sorry I did not see that anyone had replied to your postings.

I’m glad you worked it out!

Rachel.
Originally posted by Rachel Steiner:
Hi Jian,

Load a representative raw dwi dataset from your study in the GUI, go to the protocol tab, click default protocol, then click “save as” to save the xml file somewhere before clicking “Run.” You can modify the default parameters right there in the GUI then save it again as the new modified xml without running the whole processing. Just click save rather Jan run protocol.

Alternatively, run a new dtiprep window to open up that default xml file younjust saved and manually modify using the GUI and then save as a different name somewhere safely to be used on the command line ... on the command line you will be pointing the -p to the absolute path where you’ve saved the modified xml. For example, /Home/safe/modified. xml

Did I understand your question correctly? Are you having an issue finding a save as button in the GUI window with your version of dtiprep?

Rachel



color=#000000]
[/color]Originally posted by Jian Zhang:
Hi experts,

We want to use the command line of DTIPrep to create XML file and then modify it, using the command as below:
DTIPrep -d -p SomeProto.xml -w dwi.nrrd
But, only the GUI of DTIPrep will be launched, so we set the command like this:
DTIPrep -d -c -p SomeProto.xml -w dwi.nrrd
We got the default protocol file, but this command run the whole quality check procedure!
Can you help us to point out how to create the default protocol XML file via command, without running the whole quality check, so that we can quickly modify XML file and then run the next command:
DTIPrep -c -p Modified.xml -w dwi.nrrd
OR is there any way to combine these 2 steps together?

Thank you very much!

-Jian
Feb 12, 2018  09:02 AM | Jian Zhang
RE: Create XML file without running checking
Hi Martin,

Just as a follow up, which option should we choose to turn off the checking of gradient directions? Change the "IMAGE bCheck" to No or change the "DIFFUSION bCheck" to no?

Thanks
Jian
Mar 6, 2018  07:03 AM | Martin Styner
RE: Create XML file without running checking
Sorry, forgot to follow up. It's the DIFFUSION bCheck that needs to be set to "No"
Best
Martin
Originally posted by Jian Zhang:
Hi Martin,

Just as a follow up, which option should we choose to turn off the checking of gradient directions? Change the "IMAGE bCheck" to No or change the "DIFFUSION bCheck" to no?

Thanks
Jian
Mar 9, 2018  08:03 AM | Jian Zhang
RE: Create XML file without running checking
Thanks, Martin. It's clear now.

Jian
Originally posted by Martin Styner:
Sorry, forgot to follow up. It's the DIFFUSION bCheck that needs to be set to "No"
Best
Martin
Originally posted by Jian Zhang:
Hi Martin,

Just as a follow up, which option should we choose to turn off the checking of gradient directions? Change the "IMAGE bCheck" to No or change the "DIFFUSION bCheck" to no?

Thanks
Jian