open-discussion > Questions about understanding QCreport
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Nov 29, 2018  09:11 AM | Huan Yang
Questions about understanding QCreport
Dear all,
 
After I run DTIprep, i don't understand some points in QCReport.
1. Some parameters are blank under "Interlace-wise Check Artifacts"and "Inter-gradient check Artifacts", as following:

Interlace-wise Check Artifacts:
Gradient#:       AngleX        AngleY     AngleZ       TranslationX       TranslationY    TranslationZ      Metric(MI) Correlation

Inter-gradient check Artifacts:
Gradient#:      AngleX     AngleY        AngleZ         TranslationX        TranslationY     TranslationZ        Metric(MI)

Whether there should be parameters following Anglex, et al.


2. As I seen in the QCReport, there are results of "EddyCurrentHeadMotionCorrectIowa ...
Transforms"whether that is mean the QC check has done the eddy current and head motion correction. If so how to understand the following results?
I don't understand why each included gradient has two lines, one is parameters, and the other is fixed parameters. And why the following numbers have different number, since "parameter" has 12 numbers, but "fixed parameters" has 3 numbers?

0 - Parameters: [0.9997539562179837, -0.0000456712971941987, 0.00012814643209806194, 0.0001919390366571939, 0.9996859054763518, -0.00002926969037700233, -0.00011713357421570307, 0.00010946833467130879, 0.9997676269027517, -0.0009163895499214427, -0.005300804295234882, 0.008665774469949795]
0 - Fixed Parameters: [2.0063291738889677, 29.472202481645756, -25.351412463387636]
1 - Parameters: [0.9973658126577162, -0.0032099643661705193, -0.0026982670174528984, 0.003487339476547441, 0.99321195724164, 0.011081261533761417, 0.0035208460196087398, -0.009190952090957454, 0.999104607135376, 0.06964221564603196, -0.28415220872622377, -0.7374703184740822]
1 - Fixed Parameters: [2.0063291738889677, 29.472202481645756, -25.351412463387636]

3. when we need to transfer nerd files to nil format, we should transfer the *.nrrd or *_QCed.nrrd? It seems I can only transfer *.nrrd to nil, and failed to transfer *_QCed.nrrd to nil.


Thank you so much for your help.
Huan
Nov 29, 2018  10:11 AM | Martin Styner
RE: Questions about understanding QCreport
Dear Huan
Re 1. Which file are you refering to, the "txt" file or the "xml" file. The "txt" is more information reporting, and the xml should be used if you plan to perform any analysis of the computed transforms or corrections/rejections. In general, parameters may no values for a given DWI, if a prior step excluded that DWI (so any further steps would not be applied to it).

Re 2. Both sets of parameters are used to describe the full affine transform. The fixed parameter describes center of rotation of a transform. See also:
https://itk.org/Doxygen312/html/classitk...

Best 
Martin

Originally posted by Huan Yang:
Dear all,
 
After I run DTIprep, i don't understand some points in QCReport.
1. Some parameters are blank under "Interlace-wise Check Artifacts"and "Inter-gradient check Artifacts", as following:

Interlace-wise Check Artifacts:
Gradient#:       AngleX        AngleY     AngleZ       TranslationX       TranslationY    TranslationZ      Metric(MI) Correlation

Inter-gradient check Artifacts:
Gradient#:      AngleX     AngleY        AngleZ         TranslationX        TranslationY     TranslationZ        Metric(MI)

Whether there should be parameters following Anglex, et al.


2. As I seen in the QCReport, there are results of "EddyCurrentHeadMotionCorrectIowa ...
Transforms"whether that is mean the QC check has done the eddy current and head motion correction. If so how to understand the following results?
I don't understand why each included gradient has two lines, one is parameters, and the other is fixed parameters. And why the following numbers have different number, since "parameter" has 12 numbers, but "fixed parameters" has 3 numbers?

0 - Parameters: [0.9997539562179837, -0.0000456712971941987, 0.00012814643209806194, 0.0001919390366571939, 0.9996859054763518, -0.00002926969037700233, -0.00011713357421570307, 0.00010946833467130879, 0.9997676269027517, -0.0009163895499214427, -0.005300804295234882, 0.008665774469949795]
0 - Fixed Parameters: [2.0063291738889677, 29.472202481645756, -25.351412463387636]
1 - Parameters: [0.9973658126577162, -0.0032099643661705193, -0.0026982670174528984, 0.003487339476547441, 0.99321195724164, 0.011081261533761417, 0.0035208460196087398, -0.009190952090957454, 0.999104607135376, 0.06964221564603196, -0.28415220872622377, -0.7374703184740822]
1 - Fixed Parameters: [2.0063291738889677, 29.472202481645756, -25.351412463387636]


Thank you so much for your help.
Huan