RFC: Fix NRRD output axis order#356
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hjmjohnson merged 2 commits intoBRAINSia:masterfrom Nov 29, 2017
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@ihnorton Thank you very much for doing this testing. I will test as soon as I can. |
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Tests run and passed. |
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@ihnorton Thanks for your support. Code confirmed. |
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Thanks: Isaiah Norton <inorton@bwh.harvard.edu> References: * BRAINSia/BRAINSTools#356 * https://discourse.slicer.org/t/dti-nifti-data-import-via-dwi-convert-module/1460/4 List of changes: $ git shortlog 42ac3c3..c1289e6 --no-merges Hans J. Johnson (1): ENH: Need to add allowLossy for file types other than short. Isaiah Norton (2): BUG: ITK is row-major; fix NRRD output with mismatched (x,y) axis sizes BUG: FSL converter should check reader status git-svn-id: http://svn.slicer.org/Slicer4/trunk@26676 3bd1e089-480b-0410-8dfb-8563597acbee
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Thanks: Isaiah Norton <inorton@bwh.harvard.edu> References: * BRAINSia/BRAINSTools#356 * https://discourse.slicer.org/t/dti-nifti-data-import-via-dwi-convert-module/1460/4 List of changes: $ git shortlog 42ac3c3..c1289e6 --no-merges Hans J. Johnson (1): ENH: Need to add allowLossy for file types other than short. Isaiah Norton (2): BUG: ITK is row-major; fix NRRD output with mismatched (x,y) axis sizes BUG: FSL converter should check reader status git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26767 3bd1e089-480b-0410-8dfb-8563597acbee
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Thanks: Isaiah Norton <inorton@bwh.harvard.edu> References: * BRAINSia/BRAINSTools#356 * https://discourse.slicer.org/t/dti-nifti-data-import-via-dwi-convert-module/1460/4 List of changes: $ git shortlog 42ac3c3..c1289e6 --no-merges Hans J. Johnson (1): ENH: Need to add allowLossy for file types other than short. Isaiah Norton (2): BUG: ITK is row-major; fix NRRD output with mismatched (x,y) axis sizes BUG: FSL converter should check reader status git-svn-id: http://svn.slicer.org/Slicer4/trunk@26676 3bd1e089-480b-0410-8dfb-8563597acbee
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Thanks: Isaiah Norton <inorton@bwh.harvard.edu> References: * BRAINSia/BRAINSTools#356 * https://discourse.slicer.org/t/dti-nifti-data-import-via-dwi-convert-module/1460/4 List of changes: $ git shortlog 42ac3c3..c1289e6 --no-merges Hans J. Johnson (1): ENH: Need to add allowLossy for file types other than short. Isaiah Norton (2): BUG: ITK is row-major; fix NRRD output with mismatched (x,y) axis sizes BUG: FSL converter should check reader status svn-url: http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=26767 git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26767 3bd1e089-480b-0410-8dfb-8563597acbee
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Thanks: Isaiah Norton <inorton@bwh.harvard.edu> References: * BRAINSia/BRAINSTools#356 * https://discourse.slicer.org/t/dti-nifti-data-import-via-dwi-convert-module/1460/4 List of changes: $ git shortlog 42ac3c3..c1289e6 --no-merges Hans J. Johnson (1): ENH: Need to add allowLossy for file types other than short. Isaiah Norton (2): BUG: ITK is row-major; fix NRRD output with mismatched (x,y) axis sizes BUG: FSL converter should check reader status git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-8@26767 3bd1e089-480b-0410-8dfb-8563597acbee
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NOTE: small change -- but please review very carefully and see note below
This turned out to be a little more involved than the pixel precision mismatch I initially suspected: NRRD output size axes appear to be swapped relative to ITK row-major array storage (and have been back at least 5 years or so). In practice, this only matters when x and y axis dimensions are different -- as they happen to be in this particular dataset I was sent after a Slicer forum post.
Input nifti dimensions: 173 207 173 143
Output nrrd - before:
sizes: 207 173 173 143Output nrrd - after:
sizes: 173 207 173 143Apparently such an acquisition is relatively rare, though I'm still surprised this could have persisted for so long. As such, despite fixing read of this particular dataset, there's a chance I missed some underlying assumption elsewhere in the code. So, please review carefully and run the test suite if possible before merging. I'm not set up to run it myself right now, but if needed I can set it up to run on our cluster if it can't otherwise be run.