open-discussion > Extract FA and MD maps calculated by DTIPrep
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Feb 21, 2019  03:02 AM | esin karahan - Cardiff University Brain Research Imaging Centre
Extract FA and MD maps calculated by DTIPrep
Hi DTIPrep developers,

I am using DTIPrep Version 1.2.8.

My DWI data is composed of 30 directions of b=1200 shell and 60 directions of b=2400 shell. I ran a DTIPrep QC check over all my subjects. I want to compare the FA/MD maps between DTIPrep pipeline and a standard FSL DITFIT pipeline (bet, eddt_correct, linear dtifit) to see how much FA/MD maps are affected by the correction.

I have 2 questions:

1 - Is it possible to calculate FA/MD values in DTIPrep by only using one shell data (b=1200) by quality checking on the whole dataset?

2 - How can I export the FA/MD maps from the *_QCed.nrrd file to NIFTI fileformat?

I used the Slicer DWIConvert NRRD2FSL option bu it gave me the following error:

======= DWI Convert Tool Program=========
INPUT VOLUME: ~/QC/checked/p1_QCed.nrrd
Error: ReadVolume: Unsupported source pixel type.
Input volume: unsigned_short
Output volume: short
The only supported output type is . You may consider using allowLossyConversion option.
However, use this option with caution! Conversion from images of a different type may cause data loss due to rounding or truncation.
terminate called after throwing an instance of 'itk::ExceptionObject'
what(): /work/Stable/Slicer-4101-build/BRAINSTools/DWIConvert/DWIConvertLib.cxx:130:
itk::ERROR: Exception creating converter
itk::ExceptionObject (0x25a1550)
Location: "unknown"
File: /work/Stable/Slicer-4101-build/BRAINSTools/DWIConvert/NRRDDWIConverter.cxx
Line: 91
Description: itk::ERROR: ERROR Reading NRRD File : ~/QC/checked/p1_QCed.nrrd

Thanks a lot.
Esin
Feb 21, 2019  05:02 AM | Rachel Steiner - University of Wisconsin - Madison
RE: Extract FA and MD maps calculated by DTIPrep
Hi esin,

I believe I know the workaround. Do you mind sharing some info though:

Can you share the header information from your original nrrd DWI file from pre-QC with DTIPrep with me? And also the header info of the QCed version?

If you are unsure of how to do that, I think I can answer my own question by looking at your DTIPrep QC protocol that you ran on all of the subjects (assuming you kept the same protocol for everyone) and the DTIPrep final QC report.txt file that was output after it finished running for the p1 subject nrrd file that’s giving you problems.

What scanner manufacturer did you collect this data on? Siemens?
Feb 21, 2019  07:02 AM | esin karahan - Cardiff University Brain Research Imaging Centre
RE: Extract FA and MD maps calculated by DTIPrep
Hi Rachel,

Thank you very much for the quick response. 

I attached a zip file that contains a mat file for the header info of both pre-QC & QC-ed images,  protocol.xml and QC report. The pre-QC file was in FSL-NIFTI format and I converted to NRRD by using DWI Convert tool in Slicer (vr 4.10.1 r27931) before QC.


Best,
Esin
Attachment: p1.zip
Feb 21, 2019  07:02 AM | esin karahan - Cardiff University Brain Research Imaging Centre
RE: Extract FA and MD maps calculated by DTIPrep
Sorry I forgot to tell. It is a Siemens 3T Prisma scanner.

Thanks again.