Problem to import DWI images using Diffusion-weighted DICOM Import (DWIConvert)

shahrokh · June 3, 2019, 4:16am

Dears 3DSlicer developers:

Specification:
Fedora Core 25 (Linux localhost.localdomain 4.8.6-300.fc25.x86_64)
3DSlicer versions 4.8.1
3DSlicer versions 4.9.0
3DSlicer versions 4.10.0

I have 1768 DWI images (from ep2d__FOV256_ISO2mm_i1.dcm to ep2d__FOV256_ISO2mm_i1768.dcm), 68 slices per volume and 26 volumes

I want to use “UKF Tractogrpahy” module to analyze these image. To do this and import images, I think that I should use the module of “Diffusion-weighted DICOM Import (DWIConvert)” with the following setup.

ScreenshotDWIConvert

When I execute this module, I get the following error message:

/home/sn/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/cli-modules/DWIConvert --conversionMode DicomToNrrd --inputDicomDirectory /home/sn/Diffusion --outputNiftiFile /home/sn/Diffusion/test --outputBValues /home/sn/Diffusion/test --outputBVectors /home/sn/Diffusion/test --outputDirectory . --smallGradientThreshold 0.2 --transposeInputBVectors

Diffusion-weighted DICOM Import (DWIConvert) standard output:

======= DWI Convert Public Lib Ctest =========
=================== this->m_SlicesPerVolume:68
Dicom images are ordered in a volume interleaving way.
ImageOrientationPatient (0020:0037): LPS Orientation Matrix
0.999997 3.3575e-08 0.00238174
-0.000420449 0.984298 0.176516
-0.00234433 -0.176516 0.984295

this->m_SpacingMatrix
2 0 0
0 2 0
0 0 2

NRRDSpaceDirection
1.99999 6.71501e-08 0.00476347
-0.000840897 1.9686 0.353032
-0.00468866 -0.353033 1.96859

Slice 0: -136.139 -145.778 33.773
Slice 1: -136.135 -145.425 35.7416
Slice order is IS
Image#: 0 BV: 0 GD: 0,0,0
Number of Directions : 3
Directions 0: 0.86221
Directions 1: -0.362712
Directions 2: 0.353602
DiffusionVector_magnitude 1
Image#: 68 BV: 1000 GD: 0.86220956,-0.36271203,0.35360244
Number of Directions : 3
Directions 0: 0.863006
Directions 1: 0.36176
Directions 2: 0.352634
DiffusionVector_magnitude 1
Image#: 136 BV: 1000 GD: 0.86300552,0.36176044,0.35263431
Number of Directions : 3
Directions 0: 0.862383
Directions 1: 0.362935
Directions 2: -0.352951
DiffusionVector_magnitude 1
Image#: 204 BV: 1000 GD: 0.86238289,0.36293468,-0.35295057
Number of Directions : 3
Directions 0: 0.863359
Directions 1: -0.361339
Directions 2: -0.352202
DiffusionVector_magnitude 1
Image#: 272 BV: 1000 GD: 0.8633585,-0.36133933,-0.35220158
Number of Directions : 3
Directions 0: 0.357315
Directions 1: -0.361901
Directions 2: -0.861019
DiffusionVector_magnitude 1
Image#: 340 BV: 1000 GD: 0.35731497,-0.3619009,-0.86101902
Number of Directions : 3
Directions 0: 0.356462
Directions 1: -0.865857
Directions 2: -0.351035
DiffusionVector_magnitude 1
Image#: 408 BV: 1000 GD: 0.35646203,-0.86585736,-0.35103545
Number of Directions : 3
Directions 0: 0.355873
Directions 1: -0.865479
Directions 2: 0.352564
DiffusionVector_magnitude 1
Image#: 476 BV: 1000 GD: 0.35587266,-0.86547863,0.35256404
Number of Directions : 3
Directions 0: 0.356936
Directions 1: -0.36273
Directions 2: 0.860828
DiffusionVector_magnitude 1
Image#: 544 BV: 1000 GD: 0.35693565,-0.36272988,0.86082757
Number of Directions : 3
Directions 0: 0.357965
Directions 1: 0.361675
Directions 2: 0.860844
DiffusionVector_magnitude 1
Image#: 612 BV: 1000 GD: 0.35796461,0.36167514,0.86084408
Number of Directions : 3
Directions 0: 0.356507
Directions 1: 0.865463
Directions 2: 0.351961
DiffusionVector_magnitude 1
Image#: 680 BV: 1000 GD: 0.35650745,0.8654629,0.35196099
Number of Directions : 3
Directions 0: 0.35609
Directions 1: 0.865654
Directions 2: -0.351912
DiffusionVector_magnitude 1
Image#: 748 BV: 1000 GD: 0.35609004,0.86565441,-0.35191223
Number of Directions : 3
Directions 0: 0.357203
Directions 1: 0.363002
Directions 2: -0.860602
DiffusionVector_magnitude 1
Image#: 816 BV: 1000 GD: 0.3572031,0.36300167,-0.86060208
Image#: 884 BV: 0 GD: 0,0,0
Number of Directions : 3
Directions 0: 0.86221
Directions 1: -0.362712
Directions 2: 0.353602
DiffusionVector_magnitude 1
Image#: 952 BV: 1000 GD: 0.86220956,-0.36271203,0.35360244
Number of Directions : 3
Directions 0: 0.863006
Directions 1: 0.36176
Directions 2: 0.352634
DiffusionVector_magnitude 1
Image#: 1020 BV: 1000 GD: 0.86300552,0.36176044,0.35263431
Number of Directions : 3
Directions 0: 0.862383
Directions 1: 0.362935
Directions 2: -0.352951
DiffusionVector_magnitude 1
Image#: 1088 BV: 1000 GD: 0.86238289,0.36293468,-0.35295057
Number of Directions : 3
Directions 0: 0.863359
Directions 1: -0.361339
Directions 2: -0.352202
DiffusionVector_magnitude 1
Image#: 1156 BV: 1000 GD: 0.8633585,-0.36133933,-0.35220158
Number of Directions : 3
Directions 0: 0.357315
Directions 1: -0.361901
Directions 2: -0.861019
DiffusionVector_magnitude 1
Image#: 1224 BV: 1000 GD: 0.35731497,-0.3619009,-0.86101902
Number of Directions : 3
Directions 0: 0.356462
Directions 1: -0.865857
Directions 2: -0.351035
DiffusionVector_magnitude 1
Image#: 1292 BV: 1000 GD: 0.35646203,-0.86585736,-0.35103545
Number of Directions : 3
Directions 0: 0.355873
Directions 1: -0.865479
Directions 2: 0.352564
DiffusionVector_magnitude 1
Image#: 1360 BV: 1000 GD: 0.35587266,-0.86547863,0.35256404
Number of Directions : 3
Directions 0: 0.356936
Directions 1: -0.36273
Directions 2: 0.860828
DiffusionVector_magnitude 1
Image#: 1428 BV: 1000 GD: 0.35693565,-0.36272988,0.86082757
Number of Directions : 3
Directions 0: 0.357965
Directions 1: 0.361675
Directions 2: 0.860844
DiffusionVector_magnitude 1
Image#: 1496 BV: 1000 GD: 0.35796461,0.36167514,0.86084408
Number of Directions : 3
Directions 0: 0.356507
Directions 1: 0.865463
Directions 2: 0.351961
DiffusionVector_magnitude 1
Image#: 1564 BV: 1000 GD: 0.35650745,0.8654629,0.35196099
Number of Directions : 3
Directions 0: 0.35609
Directions 1: 0.865654
Directions 2: -0.351912
DiffusionVector_magnitude 1
Image#: 1632 BV: 1000 GD: 0.35609004,0.86565441,-0.35191223
Number of Directions : 3
Directions 0: 0.357203
Directions 1: 0.363002
Directions 2: -0.860602
DiffusionVector_magnitude 1
Image#: 1700 BV: 1000 GD: 0.3572031,0.36300167,-0.86060208

Diffusion-weighted DICOM Import (DWIConvert) standard error:

Error: the output file type is not supported currently
Error: the output file type is not supported currently
Invalidate conversion mode
Diffusion-weighted DICOM Import (DWIConvert) completed with errors

I must mention that I get the same error in 3DSlicer versions 4.8.1, 4.9.0 and 4.10.0.
Please guide me.

Please guide me.
Thanks a lot.
Shahrokh

ljod · June 3, 2019, 11:19am

Please use the new release 4.10.2 and the new module dcm2niix GUI. This should load a much more comprehensive set of recent DICOM DWI.

Let us know if this works for you.

shahrokh · June 3, 2019, 1:00pm

Dear Lauren

Thank you very very much. This is an excellent version. My problem was solved.
Best regards.

ljod · June 3, 2019, 1:55pm

Great!! Thanks for letting us know that the new release solves this issue.

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Problem to import DWI images using Diffusion-weighted DICOM Import (DWIConvert)

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