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

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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
RE: DWIConvert
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
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Maike Kleemeyer Jan 10, 2018
Martin Styner Jan 10, 2018
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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