LCModel IO - "VOLUME = NaN" #145
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Hi @bkossows, this will be a problem with loading the transform data so Suspect doesn't know the voxel dimensions so when it exports it leaves this NaN for volume. Or possibly with some kind of corruption of the transform. What happens if you just run |
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I will send You the file by an email. print(data.transform) [[ nan nan nan -0.586961] |
bennyrowland
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This code addresses an issue reported in #145 for Siemens twix files where voxels prescribed sagittally calculate a transform of NaNs. This arises because in the twix file the row and column axes are not specified, but must be calculated from the normal and a rotation from a starting pair of axes. This starting pair of axes is not consistent but depends on how the voxel was planned. In turn this is not described in the file but must be deduced from the normal vector. The new code is an attempt to solve this problem for the data files where an issue has been reported, but may not be correct for some other class of twix files.
bennyrowland
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This code addresses an issue reported in #145 for Siemens twix files where voxels prescribed sagittally calculate a transform of NaNs. This arises because in the twix file the row and column axes are not specified, but must be calculated from the normal and a rotation from a starting pair of axes. This starting pair of axes is not consistent but depends on how the voxel was planned. In turn this is not described in the file but must be deduced from the normal vector. The new code is an attempt to solve this problem for the data files where an issue has been reported, but may not be correct for some other class of twix files. Fixes #145
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bennyrowland
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* #BUG Sag voxels in twix fail to calculate a transform This code addresses an issue reported in #145 for Siemens twix files where voxels prescribed sagittally calculate a transform of NaNs. This arises because in the twix file the row and column axes are not specified, but must be calculated from the normal and a rotation from a starting pair of axes. This starting pair of axes is not consistent but depends on how the voxel was planned. In turn this is not described in the file but must be deduced from the normal vector. The new code is an attempt to solve this problem for the data files where an issue has been reported, but may not be correct for some other class of twix files. * #BUG Sag voxels in twix fail to calculate a transform This code addresses an issue reported in #145 for Siemens twix files where voxels prescribed sagittally calculate a transform of NaNs. This arises because in the twix file the row and column axes are not specified, but must be calculated from the normal and a rotation from a starting pair of axes. This starting pair of axes is not consistent but depends on how the voxel was planned. In turn this is not described in the file but must be deduced from the normal vector. The new code is an attempt to solve this problem for the data files where an issue has been reported, but may not be correct for some other class of twix files. Fixes #145 * updated changelog to detail fix
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For 20% Siemens TWIX data I was unable to run LCModel analysis with an error 1 FATAL ZEROVX 4. In CONTROL file there was "VOLUME = NaN" instead of a some numerical value.
B.
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