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Empty nii from PET images #374

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lamaresh opened this issue Feb 15, 2020 · 6 comments
Closed

Empty nii from PET images #374

lamaresh opened this issue Feb 15, 2020 · 6 comments

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@lamaresh
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If I use stable branch conversion works fine.
Using development branch when I try to convert GE PET images the output is a nii file with only 0
@neurolabusc
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Hard to provide feedback without seeing an example. You could try running the development and stable builds using the -v 2 parameter and seeing if this reveal the change. I have very little experience with GE PET images, so unclear why the recent changes would have an impact.

@lamaresh
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lamaresh commented Feb 16, 2020 •
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I found the commit when it stopped working: ca47499?diff=split

@lamaresh
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I made a pull request with a possible fix
#375

@neurolabusc
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You have done a good job identifying the root problem. Unfortunately, your pull request will have unintended consequences. Specifically, you have identified that the detection of variable slice intensity scaling has issues. However, as shown in that issue, the slice scaling can vary not only between volumes, but within slices of a single volume.

neurolabusc added a commit that referenced this issue Feb 16, 2020
@neurolabusc
GE PET with variable slice intensity (#374)
1fd360b
@neurolabusc
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@lamaresh can you please test my latest commit. I have very little experience with GE PET data. I would suggest you carefully validate the resulting output and make sure my software is behaving as expected. @halfSpinDoctor may also have some thoughts on this. If anyone has a phantom or other data that can be shared, it would nice to have a validation dataset, not only for dcm2niix but for other conversion tools.

@lamaresh
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After your last commit the output nii has a "plausible" content, but I have little experience either with PET data so I can't help you validate it for sure,

yarikoptic added a commit to neurodebian/dcm2niix that referenced this issue May 6, 2020
@yarikoptic
Merge tag 'v1.0.20200331' into debian
c51c61e 
* tag 'v1.0.20200331': (52 commits)
  Update submodules
  Update dcm_qa submodule.
  UIH 3D sequence quirk
  New release, EstimatedTotalReadoutTime/EstimatedEffectiveEchoSpacing (rordenlab#377)
  Philips TotalReadoutTime (rordenlab#377)
  Cleanup
  Experimental Canon DICOM support (rordenlab#388)
  Experimental solution for issue 384 (rordenlab#384)
  Detect catastrophic anonymization (rordenlab#383)
  Only report "multiple inversion times" if 0018,9079 values differ (e.g. Bangalore data in https://github.com/neurolabusc/dcm_qa_philips)
  Consistent echo naming (rordenlab#381)
  Philips partial Fourier (rordenlab#377)
  Support InversionTImes (0018,9079) tag (rordenlab#380)
  Philips effective echo spacing formula ambiguous (rordenlab#377)
  TR for Philips 3D EPI (rordenlab#369)
  Citation (rordenlab#102)
  GE PET with variable slice intensity (rordenlab#374)
  Estimate Philips EffectiveEchoSpacing (nipreps/sdcflows#5)
  GE slice interpolation (rordenlab#373)
  3D EPI TR (rordenlab#369) 3D phase (rordenlab#371) Enhanced ordering (rordenlab#372 (comment))
  ...
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@lamaresh @neurolabusc