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Inconsistent echo-1 naming for multi-echo fmri #381

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jrdalenberg opened this issue Mar 11, 2020 · 5 comments
Closed

Inconsistent echo-1 naming for multi-echo fmri #381

jrdalenberg opened this issue Mar 11, 2020 · 5 comments

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@jrdalenberg
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Version info: dcm2niix version v1.0.20190902 (JP2:OpenJPEG) (JP-LS:CharLS) Clang8.1.0 (64-bit MacOS)
Sequence: Latest CMRR sequence for a Siemens Prisma, https://www.cmrr.umn.edu/multiband/
Protocol: Multiband (MB=4), multi-echo (3 echos)

We run the same protocol multiple times across multiple subjects. For about 10-20% of the scans, the echo-1 output file is not properly named as _e1 while _e2 and _e3 are always correct. The field "EchoNumber": 1 is also missing in the json file when this happens. This seems to happen randomly within and across subjects.

Expected:

[name]_e1.nii
[name]_e1.json
[name]_e2.nii
[name]_e3.json
[name]_e3.nii
[name]_e3.json

Found:

[name].nii
[name].json
[name]_e2.nii
[name]_e3.json
[name]_e3.nii
[name]_e3.json
@neurolabusc
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Can you confirm the behavior is now consistent if you upgrade to the development branch. I am hoping to close one remaining issue specific to Philips images before releasing a new stable release, so this is a good time to test the development branch as is the release candidate for the next stable release.

On MacOS and Linux you can build the developmental branch with these commands:

git clone --branch development https://github.com/rordenlab/dcm2niix.git
cd dcm2niix/console
make
./dcm2niix

Windows users should be able to get a compiled version from AppVeyor.

@jrdalenberg
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jrdalenberg commented Mar 11, 2020 •
edited

Version: v1.0.20200229 Clang11.0.0 (64-bit MacOS)

> ~/dcm2niix/console/dcm2niix ./
...
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 5 DICOM as ./__MBME_dir-PA_20200206100603_7_e3 (64x64x48x5)
Convert 5 DICOM as ./__MBME_dir-PA_20200206100603_7_e1 (64x64x48x5)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 5 DICOM as ./__MBME_dir-PA_20200206100603_7_e2 (64x64x48x5)
Convert 540 DICOM as ./__rest1MBME_20200206100603_6 (64x64x48x540)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 540 DICOM as ./__rest1MBME_20200206100603_6_e3 (64x64x48x540)
Convert 540 DICOM as ./__rest1MBME_20200206100603_6_e2 (64x64x48x540)

No, it is not :(

Edit: specific attempt on run 6

> ~/dcm2niix/console/dcm2niix ./6/
Chris Rorden's dcm2niiX version v1.0.20200229  Clang11.0.0 (64-bit MacOS)
Found 1620 DICOM file(s)
Slices not stacked: echo varies (TE 36.1, 60.2; echo 2, 3). Use 'merge 2D slices' option to force stacking
Convert 540 DICOM as ./6/6_rest1MBME_20200206100603_6_e2 (64x64x48x540)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 540 DICOM as ./6/6_rest1MBME_20200206100603_6_e3 (64x64x48x540)
Convert 540 DICOM as ./6/6_rest1MBME_20200206100603_6_e1 (64x64x48x540)
Conversion required 10.370607 seconds (3.002684 for core code).

Looks like it sometimes does not work when converting everything from a participant in one go.

@jrdalenberg
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jrdalenberg commented Mar 11, 2020 •
edited

I tried converting with and without including several of the scans.

It seems to specifically happen when there is a combination of multiple ME and one or more non-ME fMRI scans in the subject DICOM files.

> ~/dcm2niix/console/dcm2niix ./
Chris Rorden's dcm2niiX version v1.0.20200229  Clang11.0.0 (64-bit MacOS)
Found 2405 DICOM file(s)
Slices not stacked: echo varies (TE 12, 36.1; echo 1, 2). Use 'merge 2D slices' option to force stacking
Convert 260 DICOM as ./__hands1MBME_20200206100603_10 (64x64x48x260)
Convert 260 DICOM as ./__hands1MBME_20200206100603_10_e2 (64x64x48x260)
Convert 260 DICOM as ./__hands1MBME_20200206100603_10_e3 (64x64x48x260)
Convert 540 DICOM as ./__rest1MBME_20200206100603_6_e2 (64x64x48x540)
Convert 540 DICOM as ./__rest1MBME_20200206100603_6_e1 (64x64x48x540)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 540 DICOM as ./__rest1MBME_20200206100603_6_e3 (64x64x48x540)
Convert 5 DICOM as ./__MB_dir-PA_20200206100603_9 (114x114x72x5)
Conversion required 19.879055 seconds (6.241951 for core code).

See scan _10 above.

neurolabusc added a commit that referenced this issue Mar 12, 2020
@neurolabusc
Consistent echo naming (#381)
4660e75
@neurolabusc
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@jrdalenberg can you test the latest developmental commit (v1.0.20200312) to see if it resolves your issue.

@jrdalenberg
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@neurolabusc Yes it does! Thanks!

Before:

Chris Rorden's dcm2niiX version v1.0.20190902  (JP2:OpenJPEG) (JP-LS:CharLS) Clang8.1.0 (64-bit MacOS)
Found 1346 DICOM file(s)
Convert 176 DICOM as ./__MPRAGE_20200305102812_5 (240x256x176x1)
Slices not stacked: echo varies (TE 12, 36.1; echo 1, 2). Use 'merge 2D slices' option to force stacking
Convert 260 DICOM as ./__hands2MBME_20200305102812_8 (64x64x48x260)
Convert 260 DICOM as ./__hands2MBME_20200305102812_8_e2 (64x64x48x260)
Convert 260 DICOM as ./__hands2MBME_20200305102812_8_e3 (64x64x48x260)
Convert 370 DICOM as ./__rest2MB_20200305102812_6 (114x114x72x370)
Convert 5 DICOM as ./__MB_dir-PA_20200305102812_7 (114x114x72x5)
Convert 5 DICOM as ./__MBME_dir-PA_20200305102812_9_e3 (64x64x48x5)
Convert 5 DICOM as ./__MBME_dir-PA_20200305102812_9_e1 (64x64x48x5)
Convert 5 DICOM as ./__MBME_dir-PA_20200305102812_9_e2 (64x64x48x5)
Conversion required 30.887490 seconds (6.020803 for core code).

After:

Chris Rorden's dcm2niiX version v1.0.20200312  Clang11.0.0 (64-bit MacOS)
Found 1346 DICOM file(s)
Convert 176 DICOM as ./__MPRAGE_20200305102812_5 (240x256x176x1)
Slices not stacked: echo varies (TE 12, 36.1; echo 1, 2). Use 'merge 2D slices' option to force stacking
Convert 260 DICOM as ./__hands2MBME_20200305102812_8_e1 (64x64x48x260)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 260 DICOM as ./__hands2MBME_20200305102812_8_e2 (64x64x48x260)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 260 DICOM as ./__hands2MBME_20200305102812_8_e3 (64x64x48x260)
Convert 370 DICOM as ./__rest2MB_20200305102812_6 (114x114x72x370)
Convert 5 DICOM as ./__MB_dir-PA_20200305102812_7 (114x114x72x5)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 5 DICOM as ./__MBME_dir-PA_20200305102812_9_e3 (64x64x48x5)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 5 DICOM as ./__MBME_dir-PA_20200305102812_9_e1 (64x64x48x5)
UINT16->INT16 Future release will change default. github.com/rordenlab/dcm2niix/issues/338
Convert 5 DICOM as ./__MBME_dir-PA_20200305102812_9_e2 (64x64x48x5)
Conversion required 32.037006 seconds (6.080700 for core code).

@neurolabusc neurolabusc mentioned this issue Mar 31, 2020
Merged
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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@neurolabusc @jrdalenberg