Tractography issue

Support
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1

Operating system: Mac OSX Monterey
Slicer version:5.0.2
Expected behavior: Tractography visualization
Actual behavior: Errors in data import

Dear Community,

I’m trying to create a 3d model of a tractography to view the that i just received.

I followed the various tutorial provided by this community but as soon as i try to import the DICOM’s set, i notice a serie of errors.

The DICOM files that i received are without extension .dcm, .nii, nifti, nrrd

I installed the UKFTractography, SlicerDMRI and SlicerDcm2nii

Following the link of the DICOM’s set.

I think I’m doing something wrong so I hope someone with more experience could indicate me the right process to follow.

Best regards

Massimo

https://…

2

Following the errors track

Could not load: Design - as DWI Volume as a Diffusion Volume (please see DWIConvert module for advanced options and help)

Could not load: ep2d_diff_mddw_20_p2_TRACEW - as DWI Volume as a Diffusion Volume (please see DWIConvert module for advanced options and help)

Could not load: 15: ep2d_diff_mddw_20_p2_TENSOR as a Scalar Volume

Could not load: ep2d_diff_mddw_20_p2_ColFA - as a 40 frames MultiVolume by ImagePositionPatient+AcquisitionTime as a MultiVolume

3

@massimo you will need to install SlicerDMRI and make sure the dicom diffusion plugin is enabled.
From there you can load the ep2d_diff_mddw_20_p2 series and load it as DWI. From there you can do interactive and whole brain tractography and other SlicerDMRI operations. Most of the other diff series are pre-calculated from the DWI on the scanner.

4

Thanks for your kind reply,
I already installed SlicerDMRI

image
image1508×1398 141 KB

To be more accurate, i do the following:
Menu/Diffusion/Import And Export/ Tractography DICOM load

Unfortunately, during the import, I notice these serie of errors:
Could not load: Design - as DWI Volume as a Diffusion Volume (please see DWIConvert module for advanced options and help)
Could not load: ep2d_diff_mddw_20_p2_TRACEW - as DWI Volume as a Diffusion Volume (please see DWIConvert module for advanced options and help)
Could not load: 15: ep2d_diff_mddw_20_p2_TENSOR as a Scalar Volume
Could not load: ep2d_diff_mddw_20_p2_ColFA - as a 40 frames MultiVolume by ImagePositionPatient+AcquisitionTime as a MultiVolume

So cannot proceed.
Did you try to import the same serie? In case, any errors?
Thanks again
Massimo

5

I was able to load and do tractography via the DICOM module from the ep2d_diff_mddw_20_p2 series, so focus on that one and you should be able to load it too. The other series are derived data that cannot be used for tractography.

Specifically:

  • import the study into the DICOM database
  • select only the ep2d_diff_mddw_20_p2
  • in the DICOM Plugins tab be sure DICOMDiffusionVolumePlugin is select and turn off the others
  • clicking Load should load data as a diffusion volume
  • you will see the baseline volume, but if you go to the Volumes module you can scroll through the diffusion directions
  • you can then use any of the SlicerDMRI operations (tensor estmation, interactive tractography, UKF, etc)