Originally posted by Yingying Wang: to the bet2 binary and thus the second of your options

Do you know what version of Slicer the DWIConvert on the Downloads page is from? I think Slicer 4.10 introduced a new DWIConvert that fixes this issue, looking at the Slicer forum. I unfortunately am having trouble installing new full builds on my HPC.

Got it, makes sense and thanks for the tips! I have been looking at papers that cite DTIPrep, and unfortunately I am having trouble finding any that report what thresholds they used. When your group designs a protocol for the study, do you have any rules of thumb for setting these limits (particularly the interlace correlation thresholds)?

Hi Martin,

Sorry for late reply; manually changing the bvecs (in addition to the bvals which I was already doing) to 0 seemed to have worked for DTIPrep to recognize baseline scans! When I convert the QCed NRRD back to NIFTI using DWIConvert, I still see that the each bval from the output of DWIConvert always hover around the maximum bvalue (differs by no more than 0.02).

Best,
Steven

Hi Martin, Thanks for your answer,
 
      Both b0 images are removed during the slice-wiise process. It happens for all subjects, and b0 images seem to be ok when visually inspected. I modified the protocol to run only sice-wise and the problem is there. Both b0 are excluded as it is reported in the QCReport.txt and in the xml file. I am attaching the txt report.
 I guess I could use the GUI , open the xml results file and mark the b0 images as "included" after visual inspection, but doing this process for each subject would be time consuming. I hope there is another way.

Thanks in advance.

Originally posted by Martin Styner:

Originally posted by ameliaqian: It 's the z-axis slice direction (usually axial for diffusion sequences)

Martin

Hi Martin,

Thank you so much for your help! It looks like my DICOM files weren't compatible as well, but DWIConverter seems to be working with my NIFTI files. 

Best, 
Hayley

Hi Martin,

Thank you for your response:

1. I downloaded DTIPrep version 1.2.7 from the NITRC website. I am able to input the FSL bet2 path but am not sure what paths to input for the other tools. Could you provide me with the directory paths for the other tools? When I look at the package contents I cannot tell where or what files to specify.

2. With Slicer version 4.6.2 I do not see an option to add the DTIPrep extension. If is not compatible then I assume specifying where to find the tools in the standalone version of DTIPrep is the way to go? Otherwise, what version of Slicer is compatible with DTIPrep that would allow me to add as an extension?

3/4. With the output file from DTIPrep I have been trying to figure out in Slicer how to convert the image into FSL format using the DWIConverter but receive several error message. I posted the error log on the Slicer community list but have not gotten any replies. Perhaps you could help me figure out the issue. The following is the errors I receive: 



Found CommandLine Module, target is /Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert
ModuleType: CommandLineModule
DWIConverter command line:
/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --inputDicomDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --outputBValues /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvals.bval --outputBVectors /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvecs.bvec --outputDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --smallGradientThreshold 0.2
DWIConverter standard error:
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.
DWIConverter standard error:
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.
DWIConverter completed with errors
Found CommandLine Module, target is /Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert
ModuleType: CommandLineModule
DWIConverter command line:
/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeD.nrrd --inputDicomDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --outputBValues /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvals.bval --outputBVectors /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvecs.bvec --outputDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --smallGradientThreshold 0.2
DWIConverter standard error:
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.
DWIConverter completed with errors
Found CommandLine Module, target is /Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert
ModuleType: CommandLineModule
DWIConverter command line:
/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/gm/5xjgw9fs1cd6w3f79y7bj72w0000gn/T/Slicer/GHAD_vtkMRMLDiffusionWeightedVolumeNodeD.nrrd --inputDicomDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --outputBValues /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvals.bval --outputBVectors /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new/bvecs.bvec --outputDirectory /Users/MEGAN/Documents/WORK/DataAnalyses/DTI/CWANAdol/CW_0044B_4/dicom_dti/new --smallGradientThreshold 0.2
DWIConverter standard error:
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.
DWIConverter completed with errors


I checked the "Lossy Conversion" option and it ran with no errors, but my output files that were saved included the .bvec and .bval file but no NIFTI file.

Do you have a list of steps to take to convert to NIFTI format with the pipeline you use for your FSL analyses? Originally I used DWIConverter to convert my DICOM images to NRRD. And then am trying to use the NRRD to FSL option with the output from DTIPrep.

5. I did enable the sphere and gradient display as the manual shows but there is just a blank screen when I click on 3d mode. When I switch back to MPR I see the gradient I am trying to view but then nothing when I go back to 3d view. 

One other question is about the default protocol values and how to determine whether I should use the default protocol or make any changes. A tutorial I found on the NITRC site says that more information on the default protocol is available on the site but i cannot find that information. 

I'm sorry for all the questions, I am definitely a novice with these programs and recently discovered them when I was trying to figure out how to increase reliability in longitudinal TBSS studies. 

Thank you for your help,

Megan

Hi Martin, 

Thanks a lot for your suggestions!

Best, 
Karen

Hi,

Thanks Juan it works. The difference was in the step 4. I was doing ccmake rather than make.

But now when i am running the command line, it opens the GUI. I do not want to use GUI. I need to use it from command line.

./DTIPrep_build/bin/DTIPrep.app/Contents/MacOS/DTIPrep -w sub5621/data/01+dti_64dir_3x3x3/sub5621_a.nhdr -d -f working_projects/sub5621/sub5621_QC/

Any idea how to make it run via command line?

Dear Juan,

I followed the instructions below but I got an error message related to Qt

Why after I tried the command "ccmake", it always said that "command not found"?  Thank you so much if you know the answer.
Originally posted by Juan Prieto:

Originally posted by Juan Prieto:
1. git clone https://github.com/NIRALUser/DTIPrep.git
2. mkdir DTIPrep-build; cd DTIPrep-build
3. ccmake ../DTIPrep
4. make

I am able to execute first two commands without any error but in third command it is giving this error(mentioned in red colour). Please, look at it and provide appropriate solution


abhineet@abhineet-SVE15118FNB:~/DTIPrep-build$ sudo cmake ../DTIPrep
-- Found Qt4: /usr/bin/qmake (found suitable version "4.8.7", minimum required is "4.6")
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Success
-- Found Qt4: /usr/bin/qmake (found version "4.8.7")
-- SuperBuild - DTIPrepTools => Requires VTK, DCMTK, ITKv4, SlicerExecutionModel, DTIProcess, niral_utilities, BRAINSTools,
-- SuperBuild - VTK[OK]
-- SuperBuild - DCMTK[OK]
-- SuperBuild - DCMTK => Requires TIFF, JPEG, zlib,
-- SuperBuild - TIFF[OK]
-- SuperBuild - TIFF => Requires zlib, JPEG,
-- SuperBuild - zlib[OK]
-- SuperBuild - JPEG[OK]
-- SuperBuild - TIFF[OK]
-- SuperBuild - DCMTK[OK]
-- SuperBuild - ITKv4 => Requires VTK[INCLUDED], DCMTK[INCLUDED], TIFF[INCLUDED], JPEG[INCLUDED], zlib[INCLUDED],
-- SuperBuild - ITKv4[OK]
-- SuperBuild - SlicerExecutionModel => Requires ITKv4[INCLUDED],
-- SuperBuild - SlicerExecutionModel[OK]
CMake Error at SuperBuild/External_DTIProcess.cmake:36 (if):
if given arguments:

"DEFINED" "DTIProcess_DIR" "AND" "NOT" "EXISTS" "AND" "NOT" "EXISTS"
Unknown arguments specified
Call Stack (most recent call first):
CMake/SlicerMacroCheckExternalProjectDependency.cmake:69 (include)
SuperBuild.cmake:288 (SlicerMacroCheckExternalProjectDependency)
CMakeLists.txt:28 (include)
-- Configuring incomplete, errors occurred!
See also "/home/abhineet/DTIPrep-build/CMakeFiles/CMakeOutput.log".
See also "/home/abhineet/DTIPrep-build/CMakeFiles/CMakeError.log".

Hi Martin,

I specified Input Dicom Data Directory and as a Output  DWI Volume file I just selected "DWI Volume file" . I can only choose between "none" or "Rename Currect Diffusion Weigted Image" or "Create new...", "Create new as..." or "Delete ..."

So I got an following errors:

Found CommandLine Module, target is /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/DWIConvert
ModuleType: CommandLineModule
DWIConverter command line:

/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/DWIConvert --conversionMode DicomToNrrd --outputVolume /var/folders/7q/y90nswcn65sfpj6wt7h47p3c0000gn/T/Slicer/JDJ_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --inputDicomDirectory /Users/Jacek/Desktop/Tracula/dti_jacekmanko --useBMatrixGradientDirections --outputDirectory /Users/Jacek/Desktop --gradientVectorFile / --smallGradientThreshold 0.2

and this one too

DWIConverter standard error:

W: DcmItem: Length of element (6423,726d) is odd
E: DcmElement: Unknown Tag & Data (6423,726d) larger (778269289) than remaining bytes in file
E: DcmElement: Unknown Tag & Data (2020,3020) larger (808464430) than remaining bytes in file
E: DcmElement: Unknown Tag & Data (2020,3020) larger (808464430) than remaining bytes in file
/Users/..../Medphys_Asperger_20100213_s0008_i0001.dcm has no non-zero diffusion vectors
libc++abi.dylib: terminating with uncaught exception of type std::ios_base::failure: basic_filebuf::underflow error reading the file
DWIConverter terminated with an unknown exception.

Hi, just an idea,
 Try specifying the exact path where your latest version of Slicer is and add "./" before Slicer (ie: /whateverpath/Slicer-4.8somethingelse/./Slicer --launch DWIConvert.....).

Just in case you haven't done it yet.




Originally posted by Micah Johnson:

Hi Maike
DTIprep has a built-in support for multiple b-values in that it adjusts the checking parameters for the different b-values. So that should be fine.

But the default values by DTIPrep for high b-values are too strict and thus many high b-value DWIs are rejected if you use the default parameters. Best adapt them to be less strict. Double check your output, either the text report or the xml result, to see which step kicks out your DWIs (assuming they look good if you visually inspect them either with DTIPrep, Slicer or fslview), then go to the parameters for that step and increase the thresholds/sigmas.

Of course, that particular dataset may be quite bad, but you should be able to also visually see that. DTIPrep does not necessarily detect things that cannot be seen by the pure eye, but rather it standardizes & automizes the QC process (i.e. you could also visually check all your DWIs for all your datasets, which is though less stable/reliable and significantly more time consuming).

Martin

It could very well be that the issue is the data type. Not sure what DWIConvert does with float data (it probably casts it to short/Int16), as it expects short data. A possibility is that the nifti header says one thing and some FSL tag in the header says another thing (i.e. the data is actually not float, as the nifti header info is wrong).

Did you get the raw dwi data directly from the DICOM conversion? The acquired raw data should be in short, not float. Also pixdim4 should be 1 or 0 (the 4th dimension is the DWI volumes, in this case you have 33 DWIs, which have, according to fslinfo, a spacing of 8.8, which is really non-sensical as DWIs don't really have a spatial spacing), though i don't think that this is what causes DWIConvert to do something incorrect.

What conversion tool did you use (we use dcm2niix to go to nifti data from DICOM), maybe that's the issue? Alternatively you could go from DICOM to NRRD with DWIConvert, apply DTIPrep and then convert to Nifti for further processing in FSL. 

Martin

What I used was:

I think that unu is not in all Slicer versions. I found it in Slicer 4.4, so:

> cd $yourhomepathorwhatever/Slicer-4.4.0-linux-amd64/

and from there:

> ./Slicer --launch unu convert -t short -clamp -i $pathtofile/$QCednrrdfile -o $whereyouwanttheoutput/$outputfilename

(note that paths with $ need to be replaced to fit your files, without $ if they are not variables)

Hope it helps


Originally posted by Micah Johnson:

Hi James
No, you do not need those, unless you are using DTIPrep to run bet2 (in your case, you have done that already, so no need to redo it) or you want to use the Slicer based DiffusionWeightedVolumeMasking (again, not needed in your case). Thus you can safely disregard these warnings.

Best
Martin