DWI Converter error - how to convert NRRD to FSL?

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DWI Converter error - how to convert NRRD to FSL?

MeganS
Hello,
 
I am having some problems converting the output of DTIPrep .nrrd file into
FSL format.
 
In the 3D Slicer, DWI Convert I get the following error log:
 
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 <short>. 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 <short>. 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 <short>. 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 <short>. 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 not NIFTI
file.
 
I’m not sure what I am doing wrong. Any help is much appreciated.
 
Thanks,
 
Megan
 
 
 



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Re: DWI Converter error - how to convert NRRD to FSL?

inorton
Hi Megan,

I can take a look and see if there is anything we can do (that conversion may be safe if the range is in bounds for a short. DTIPrep might be changing the output datatype for no reason). I'll either suggest a fix directly or file a bug report for DWIConvert (https://github.com/BRAINSia/BRAINSTools/issues).

If you have a de-identified NRRD dataset you can share that would be helpful. Please make sure there is no protected information in the file itself or the filename. Also probably best to send directly since this mailing list is archived.

Best,
Isaiah

On Mon, Mar 6, 2017 at 1:53 PM, MeganS <[hidden email]> wrote:
Hello,

I am having some problems converting the output of DTIPrep .nrrd file into
FSL format.

In the 3D Slicer, DWI Convert I get the following error log:

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 <short>. 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 <short>. 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 <short>. 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 <short>. 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 not NIFTI
file.

I’m not sure what I am doing wrong. Any help is much appreciated.

Thanks,

Megan






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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: DWI Converter error - how to convert NRRD to FSL?

inorton
In reply to this post by MeganS
Hi Megan,

Thanks for the data. To follow up (back on the list), the underlying issue is that it is not currently possible to run DWIConvert NrrdToFSL mode from the Slicer graphical interface because the "Output Volume" selection is hard-wired to be a Slicer-created volume. I will propose a change to make GUI use possible, but it will likely take some time to become available due to other pending updates to DWIConvert.

In the meantime, the recommended option is to run DWIConvert directly from the terminal. Here is an example command line, based on the path you listed above, and run in the base directory for the zip file you sent:

/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert 
 --conversionMode NrrdToFSL --inputVolume SUBJECT_Anonymized/SUBJECT.nhdr --outputVolume nii_out/SUBJECT.nii --outputBValues nii_out/SUBJECT.bval --outputBVectors nii_out/SUBJECT.bvec --outputDirectory . --smallGradientThreshold 0.2


(command line use can also be more convenient for scripting/reproducibility)
Hope this helps.

Best,
Isaiah


On Tue, Mar 14, 2017 at 12:14 PM, Isaiah Norton <[hidden email]> wrote:
Hi Megan,

I can take a look and see if there is anything we can do (that conversion may be safe if the range is in bounds for a short. DTIPrep might be changing the output datatype for no reason). I'll either suggest a fix directly or file a bug report for DWIConvert (https://github.com/BRAINSia/BRAINSTools/issues).

If you have a de-identified NRRD dataset you can share that would be helpful. Please make sure there is no protected information in the file itself or the filename. Also probably best to send directly since this mailing list is archived.

Best,
Isaiah

On Mon, Mar 6, 2017 at 1:53 PM, MeganS <[hidden email]> wrote:
Hello,

I am having some problems converting the output of DTIPrep .nrrd file into
FSL format.

In the 3D Slicer, DWI Convert I get the following error log:

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 <short>. 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 <short>. 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 <short>. 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 <short>. 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 not NIFTI
file.

I’m not sure what I am doing wrong. Any help is much appreciated.

Thanks,

Megan






--
View this message in context: http://slicer-users.65878.n3.nabble.com/DWI-Converter-error-how-to-convert-NRRD-to-FSL-tp4031949.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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[hidden email]
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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ



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Re: DWI Converter error - how to convert NRRD to FSL?

Andras Lasso-2

Hi Isaiah,

 

Slicer just creates the volume node and then after CLI execution Slicer reads the CLI-generated output file into this volume node. Why is this causing problems for DWIConvert?

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Isaiah Norton
Sent: April 3, 2017 13:03
To: MeganS <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] DWI Converter error - how to convert NRRD to FSL?

 

Hi Megan,

 

Thanks for the data. To follow up (back on the list), the underlying issue is that it is not currently possible to run DWIConvert NrrdToFSL mode from the Slicer graphical interface because the "Output Volume" selection is hard-wired to be a Slicer-created volume. I will propose a change to make GUI use possible, but it will likely take some time to become available due to other pending updates to DWIConvert.

 

In the meantime, the recommended option is to run DWIConvert directly from the terminal. Here is an example command line, based on the path you listed above, and run in the base directory for the zip file you sent:

 

/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert 

 --conversionMode NrrdToFSL --inputVolume SUBJECT_Anonymized/SUBJECT.nhdr --outputVolume nii_out/SUBJECT.nii --outputBValues nii_out/SUBJECT.bval --outputBVectors nii_out/SUBJECT.bvec --outputDirectory . --smallGradientThreshold 0.2

 

 

(command line use can also be more convenient for scripting/reproducibility)

Hope this helps.

 

Best,

Isaiah

 

On Tue, Mar 14, 2017 at 12:14 PM, Isaiah Norton <[hidden email]> wrote:

Hi Megan,

 

I can take a look and see if there is anything we can do (that conversion may be safe if the range is in bounds for a short. DTIPrep might be changing the output datatype for no reason). I'll either suggest a fix directly or file a bug report for DWIConvert (https://github.com/BRAINSia/BRAINSTools/issues).

 

If you have a de-identified NRRD dataset you can share that would be helpful. Please make sure there is no protected information in the file itself or the filename. Also probably best to send directly since this mailing list is archived.

 

Best,

Isaiah

 

On Mon, Mar 6, 2017 at 1:53 PM, MeganS <[hidden email]> wrote:

Hello,

I am having some problems converting the output of DTIPrep .nrrd file into
FSL format.

In the 3D Slicer, DWI Convert I get the following error log:

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 <short>. 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 <short>. 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 <short>. 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 <short>. 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 not NIFTI
file.

I’m not sure what I am doing wrong. Any help is much appreciated.

Thanks,

Megan






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Re: DWI Converter error - how to convert NRRD to FSL?

inorton
In reply to this post by inorton
Hi Andras,

The "Output Volume" parameter has the CLI type "diffusion-weighted", which uses NRRD i/o. However, this parameter is dual-purposed in DWIConvert depending on the operation.

- For converting DWI DICOM -> NRRD, the CLI-created volume node you mention works fine.

- But for NRRD -> Nifti, there is no way to provide a Nifti filename, and the CLI doesn't support Nifti. (temporary CLI-created Nifti would not be useful anyway because people want to read it outside Slicer, so output needs to be retained and sent to a specific directory).

The simplest solution is to add a parameter to the NRRD -> FSL advanced section to specify the output Nifti filename, similar to the selections available for output bvec and bval paths (which can be calculated and made optional once we require specifying the Nifti filename).

Thanks,
Isaiah


On Mon, Apr 3, 2017 at 2:43 PM, Andras Lasso <[hidden email]> wrote:

Hi Isaiah,

 

Slicer just creates the volume node and then after CLI execution Slicer reads the CLI-generated output file into this volume node. Why is this causing problems for DWIConvert?

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Isaiah Norton
Sent: April 3, 2017 13:03
To: MeganS <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] DWI Converter error - how to convert NRRD to FSL?

 

Hi Megan,

 

Thanks for the data. To follow up (back on the list), the underlying issue is that it is not currently possible to run DWIConvert NrrdToFSL mode from the Slicer graphical interface because the "Output Volume" selection is hard-wired to be a Slicer-created volume. I will propose a change to make GUI use possible, but it will likely take some time to become available due to other pending updates to DWIConvert.

 

In the meantime, the recommended option is to run DWIConvert directly from the terminal. Here is an example command line, based on the path you listed above, and run in the base directory for the zip file you sent:

 

/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert 

 --conversionMode NrrdToFSL --inputVolume SUBJECT_Anonymized/SUBJECT.nhdr --outputVolume nii_out/SUBJECT.nii --outputBValues nii_out/SUBJECT.bval --outputBVectors nii_out/SUBJECT.bvec --outputDirectory . --smallGradientThreshold 0.2

 

 

(command line use can also be more convenient for scripting/reproducibility)

Hope this helps.

 

Best,

Isaiah

 

On Tue, Mar 14, 2017 at 12:14 PM, Isaiah Norton <[hidden email]> wrote:

Hi Megan,

 

I can take a look and see if there is anything we can do (that conversion may be safe if the range is in bounds for a short. DTIPrep might be changing the output datatype for no reason). I'll either suggest a fix directly or file a bug report for DWIConvert (https://github.com/BRAINSia/BRAINSTools/issues).

 

If you have a de-identified NRRD dataset you can share that would be helpful. Please make sure there is no protected information in the file itself or the filename. Also probably best to send directly since this mailing list is archived.

 

Best,

Isaiah

 

On Mon, Mar 6, 2017 at 1:53 PM, MeganS <[hidden email]> wrote:

Hello,

I am having some problems converting the output of DTIPrep .nrrd file into
FSL format.

In the 3D Slicer, DWI Convert I get the following error log:

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 <short>. 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 <short>. 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 <short>. 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 <short>. 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 not NIFTI
file.

I’m not sure what I am doing wrong. Any help is much appreciated.

Thanks,

Megan






--
View this message in context: http://slicer-users.65878.n3.nabble.com/DWI-Converter-error-how-to-convert-NRRD-to-FSL-tp4031949.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

 

 



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: DWI Converter error - how to convert NRRD to FSL?

Andras Lasso-2
In reply to this post by inorton

Thanks for the clarification. Yes, for exporting data to file from CLI, using “file” element is the right thing to do.

 

Andras

 

From: Isaiah Norton [mailto:[hidden email]]
Sent: April 3, 2017 15:10
To: Andras Lasso <[hidden email]>
Cc: MeganS <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] DWI Converter error - how to convert NRRD to FSL?

 

Hi Andras,

 

The "Output Volume" parameter has the CLI type "diffusion-weighted", which uses NRRD i/o. However, this parameter is dual-purposed in DWIConvert depending on the operation.

 

- For converting DWI DICOM -> NRRD, the CLI-created volume node you mention works fine.

 

- But for NRRD -> Nifti, there is no way to provide a Nifti filename, and the CLI doesn't support Nifti. (temporary CLI-created Nifti would not be useful anyway because people want to read it outside Slicer, so output needs to be retained and sent to a specific directory).

 

The simplest solution is to add a parameter to the NRRD -> FSL advanced section to specify the output Nifti filename, similar to the selections available for output bvec and bval paths (which can be calculated and made optional once we require specifying the Nifti filename).

 

Thanks,

Isaiah

 

 

On Mon, Apr 3, 2017 at 2:43 PM, Andras Lasso <[hidden email]> wrote:

Hi Isaiah,

 

Slicer just creates the volume node and then after CLI execution Slicer reads the CLI-generated output file into this volume node. Why is this causing problems for DWIConvert?

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Isaiah Norton
Sent: April 3, 2017 13:03
To: MeganS <
[hidden email]>
Cc: SPL Slicer Users <
[hidden email]>
Subject: Re: [slicer-users] DWI Converter error - how to convert NRRD to FSL?

 

Hi Megan,

 

Thanks for the data. To follow up (back on the list), the underlying issue is that it is not currently possible to run DWIConvert NrrdToFSL mode from the Slicer graphical interface because the "Output Volume" selection is hard-wired to be a Slicer-created volume. I will propose a change to make GUI use possible, but it will likely take some time to become available due to other pending updates to DWIConvert.

 

In the meantime, the recommended option is to run DWIConvert directly from the terminal. Here is an example command line, based on the path you listed above, and run in the base directory for the zip file you sent:

 

/Applications/Slicer.app/Contents/lib/Slicer-4.6/cli-modules/DWIConvert 

 --conversionMode NrrdToFSL --inputVolume SUBJECT_Anonymized/SUBJECT.nhdr --outputVolume nii_out/SUBJECT.nii --outputBValues nii_out/SUBJECT.bval --outputBVectors nii_out/SUBJECT.bvec --outputDirectory . --smallGradientThreshold 0.2

 

 

(command line use can also be more convenient for scripting/reproducibility)

Hope this helps.

 

Best,

Isaiah

 

On Tue, Mar 14, 2017 at 12:14 PM, Isaiah Norton <[hidden email]> wrote:

Hi Megan,

 

I can take a look and see if there is anything we can do (that conversion may be safe if the range is in bounds for a short. DTIPrep might be changing the output datatype for no reason). I'll either suggest a fix directly or file a bug report for DWIConvert (https://github.com/BRAINSia/BRAINSTools/issues).

 

If you have a de-identified NRRD dataset you can share that would be helpful. Please make sure there is no protected information in the file itself or the filename. Also probably best to send directly since this mailing list is archived.

 

Best,

Isaiah

 

On Mon, Mar 6, 2017 at 1:53 PM, MeganS <[hidden email]> wrote:

Hello,

I am having some problems converting the output of DTIPrep .nrrd file into
FSL format.

In the 3D Slicer, DWI Convert I get the following error log:

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 <short>. 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 <short>. 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 <short>. 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 <short>. 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 not NIFTI
file.

I’m not sure what I am doing wrong. Any help is much appreciated.

Thanks,

Megan






--
View this message in context: http://slicer-users.65878.n3.nabble.com/DWI-Converter-error-how-to-convert-NRRD-to-FSL-tp4031949.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
slicer-users mailing list
[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

 

 

 


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ