open-discussion > The created tutorialProtocol.xml file not suitable for other subjects
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Mar 12, 2018  12:03 PM | XIAO YANG
The created tutorialProtocol.xml file not suitable for other subjects
Hi experts,

We are now using the DTIPrep to do the quality control for DTI images. We met a problem when we tried to apply the tutorialProtocal.xml file to other subjects.

1. We used DTIPrep in the Linux and opened the .nrrd file of the first subject of out project (Sub001) to create the tutorialProtocol.xml following the guide by Dave Welch, Joy Matsui (https://www.slicer.org/w/images/a/a6/DTI...). We can use the tutorialProtocol.xml and run it for the Sub001 without any errors (no matter in the GUI or in the command). It created 10 new files (however as tutorial said, only 3 files will be created) . Though we can ignore this and just use 3 among them (DTI_Sub001_QCed.nrrd; DTI_Sub001_QCReport.txt; DTI_Sub001_XMLQCResult.xml; ), we were wondering whether this was kind of error? 10 files were as following:

DTI_Sub001_QCed_DTI_frobeniusnorm.nrrd
DTI_Sub001_QCed_DTI_MD.nrrd
DTI_Sub001_QCed_DTI.nrrd
DTI_Sub001_QCed_IDWI.nrrd
DTI_Sub001_QCed_Baseline.nrrd
DTI_Sub001_QCed.nrrd
DTI_Sub001_QCed_DTI_colorFA.nrrd
DTI_Sub001_QCReport.txt
DTI_Sub001_QCed_DTI_FA.nrrd
DTI_Sub001_XMLQCResult.xml

2. As the tutorial said, we just need to create one tutorial protocol for all subjects in one project. But when we tried to apply this tutorial (Created from the Sub01) for other subjects, it didn't work well.
Only 2 files were generated (DTI_Sub004_QCReport.txt;DTI_Sub004_XMLQCResult.xml ).

=================================
* DWI QC Report ( DTIPrep 1.2.4 ) *
=================================
DWI File: /data/xyang/test_tutorial_protocol_common/Sub004/DTI_Sub004.nrrd
xml File: /data/xyang/test_tutorial_protocol_common/Sub004/DTI_Sub004_XMLQCResult.xml
Check Time: Mon Mar 12 15:31:42 2018

Image_information_checkingImage_size_check OK
Image_information_checkingImage_origin_check FAILED
Image_information_checkingImage_spacing_check OK
Image_information_checkingImage_space_check OK
================================
Diffusion Information checking
================================
DWMRI_bValue Check: OK
DWMRI_gradient_0001 mismatch! DWI: [ 00.669879 -0.66989200000000004 -0.246644 ] protocol: [ 0.72837700000000005 -0.63302800000000004 -0.17624400000000001 ] Colinearity angle (degrees): 5.7705994761850414 > 1
DWMRI_gradient_0002 mismatch! DWI: [ -0.020227999999999999 00.387932 0.67747000000000002 ] protocol: [ 00.052897 00.449959 0.70582299999999998 ] Colinearity angle (degrees): 5.7800619388441508 > 1
DWMRI_gradient_0003 mismatch!
......
......
DWMRI_gradient_0032 mismatch! DWI: [ 0.80618999999999996 00.120661 0.70087900000000003 ] protocol: [ 00.768204 0.084681000000000006 0.71373799999999998 ] Colinearity angle (degrees): 2.6242412713547631 > 1
Diffusion gradient Check: FAILED
Diffusion information Check FAILED.

We didn't know why this happened. Was something wrong when we created the .xml file?

Any help are appreciated.

Best

Xiao
Mar 13, 2018  02:03 PM | Martin Styner
RE: The created tutorialProtocol.xml file not suitable for other subjects
Re 1. The additional files are the reconstructed tensor and its properties. So, no error.

Re 2. The error stems from the mismatch in gradients between the files. I.e. if the DWI file that you use to create the default protocol has different gradients from the DWI that you are QC\'ing then DTIPrep will raise that as an issue. Simply turn off the diffusion gradient information check and DTIPrep will not check that the protocol and the DWI have to have the same gradients.

Best
Martin
Mar 13, 2018  03:03 PM | XIAO YANG
RE: The created tutorialProtocol.xml file not suitable for other subjects
Hi Martin´╝î

Thank you very much.

There are two options available: DIFFUSION_bCheck and GRADIENT_bCheck. I tried to change the value of DIFFUSION_bCheck to 'No' when created the tutorialProtocol.xml. The tutorialProtocol.xml can be applied to other subjects without any errors. Is that the right option I changed?

Thanks again for your help.

Best
Xiao
Mar 14, 2018  04:03 AM | Martin Styner
RE: The created tutorialProtocol.xml file not suitable for other subjects
Correct, it's the DIFFUSION_bCheck that enables/disable the checking of the diffusion gradient information. The other one, GRADIENT_bCheck, is probably not well named, as it checks for residual motion present in the gradient, after motion has been corrected
Martin
Mar 14, 2018  07:03 AM | XIAO YANG
RE: The created tutorialProtocol.xml file not suitable for other subjects
Thank you so much. I got it.

I also met another problem which followed up the 'Bad gradients cannot be manual exclusion' question in the forum. 

I found a bad gradient and selected 'Exclude'. However, when I tried to save it, the pop-up box showed "No Processing done", and the changes can not be saved. I am currently using the DTIPrep1.2.4_linux64 (Qt4).

I think this may be a similar with that topic, so I put details in under that question which created by Huanjie Li. Here is the link:

https://www.nitrc.org/forum/forum.php?th...

Can you help me with that?

Xiao