open-discussion
open-discussion > RE: DWIConvert
Jan 26, 2018 02:01 AM | Martin Styner
RE: DWIConvert
It could very well be that the issue is the data type. Not sure
what DWIConvert does with float data (it probably casts it to
short/Int16), as it expects short data. A possibility is that the
nifti header says one thing and some FSL tag in the header says
another thing (i.e. the data is actually not float, as the nifti
header info is wrong).
Did you get the raw dwi data directly from the DICOM conversion? The acquired raw data should be in short, not float. Also pixdim4 should be 1 or 0 (the 4th dimension is the DWI volumes, in this case you have 33 DWIs, which have, according to fslinfo, a spacing of 8.8, which is really non-sensical as DWIs don't really have a spatial spacing), though i don't think that this is what causes DWIConvert to do something incorrect.
What conversion tool did you use (we use dcm2niix to go to nifti data from DICOM), maybe that's the issue? Alternatively you could go from DICOM to NRRD with DWIConvert, apply DTIPrep and then convert to Nifti for further processing in FSL.
Martin
Did you get the raw dwi data directly from the DICOM conversion? The acquired raw data should be in short, not float. Also pixdim4 should be 1 or 0 (the 4th dimension is the DWI volumes, in this case you have 33 DWIs, which have, according to fslinfo, a spacing of 8.8, which is really non-sensical as DWIs don't really have a spatial spacing), though i don't think that this is what causes DWIConvert to do something incorrect.
What conversion tool did you use (we use dcm2niix to go to nifti data from DICOM), maybe that's the issue? Alternatively you could go from DICOM to NRRD with DWIConvert, apply DTIPrep and then convert to Nifti for further processing in FSL.
Martin
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Title | Author | Date |
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Jacek M | Apr 8, 2016 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Martin Styner | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Ryan H | Jan 23, 2018 | |
Martin Styner | Jan 26, 2018 | |
Ryan H | Jan 26, 2018 | |
Martin Styner | Jan 26, 2018 | |
Ryan H | Jan 26, 2018 | |
Martin Styner | Jan 26, 2018 | |
Ryan H | Jan 26, 2018 | |
Martin Styner | Jan 29, 2018 | |
Ryan H | Jan 29, 2018 | |
Martin Styner | Jan 30, 2018 | |
Ryan H | Jan 30, 2018 | |
Martin Styner | Jan 31, 2018 | |
Ryan H | Feb 2, 2018 | |
Martin Styner | Feb 19, 2018 | |
Ryan H | Feb 19, 2018 | |
Martin Styner | Feb 21, 2018 | |
Ryan H | Jan 31, 2018 | |
Maike Kleemeyer | Jan 10, 2018 | |
Martin Styner | Jan 10, 2018 | |
Maike Kleemeyer | Jan 11, 2018 | |
Martin Styner | Jan 11, 2018 | |
Maike Kleemeyer | Jan 15, 2018 | |
Martin Styner | Jan 17, 2018 | |
Maike Kleemeyer | Jan 18, 2018 | |
Martin Styner | Jan 18, 2018 | |
Marie Drottar | Jun 7, 2016 | |
Jacek M | Apr 27, 2016 | |
Martin Styner | Apr 27, 2016 | |
Jacek M | Apr 15, 2016 | |
Martin Styner | Apr 15, 2016 | |
Micah Johnson | Mar 27, 2018 | |
Daniel Berge | Apr 2, 2018 | |
Micah Johnson | Apr 2, 2018 | |
Juan Prieto | Apr 8, 2016 | |
Jacek M | Apr 13, 2016 | |
Martin Styner | Apr 13, 2016 | |
Jacek M | Apr 13, 2016 | |
Martin Styner | Apr 8, 2016 | |