styner
commented
6 months ago Not sure what exactly the issue is as we are not able to reproduce it on our end with a dataset. There is a work around, as the error suggest your NRRD file has one dimension too many in space directions in the header. You can just load the NRRD file into an editor (e.g. vi) and remove one of the "none" in space direction (there should only be one dimension that has "none" for space directions, which is the 4th dimension)
funckjose1999
Hi,
I used dmriprep 0.5.7 with slice check, interlace check, susceptibility correction, eddy motion correction, brain tractography, image filter (b = 1600) and DTI estimate to run subjects. Then in the main folder, I got the copied QCed nrrd file from output.nrrd in eddymotion folder. When I tried to open the file with itk-SNAP (4.2.0 alpha3 and older version 3.8.0) and Slicer 5.6.1, the QCed nrrd file cannot be open successfully with the following error. However, with the output.nrrd, it worked well.
Exception: /Users/pauly/tk/buildbot/Nightly/itk/v5.2.1/itk/ Modules/IO/NRRD/src/itkNrrdlmage/O.cxx:292:itk::ERROR:NrrdlmagelO(0x7fad84a5bdc0): ReadImagelnformation: Error reading /Volumes/T7 Shield/masterthesis/memobaby_output/sub- buss2408/sub-buss2408_QCed.nrrd: [nrrd] nrrdLoad: trouble reading "/Volumes/T7 Shield/ masterthesis/memobabyoutput/sub-buss2408/sub-buss2408 QCed.nrrd" [nrrd] nrrdRead: trouble [nrrd] _nrrdRead: trouble reading NRRD file [nrrd] _nrrdFormatNRRD_read: trouble parsing space directions info |(1.4260179996490479,2.6729258806312828e-08,-0.46526607871055603) (-0.055397503077983856 -1.48932945728302,-0.16979075968265533) (0.46195626258850098,-0.17859950661659241,1.4158737659454346) none none [nrrd] nrrdReadNrrdParse_space_directions: seem to have more than expected 4 directions
I checked itk-SNAP and Slicer with other files, they worked well. Therefore, I am wondering if there is something wrong with dmriprep processing and the copy-paste process.
I would appreciate if the problem can be figured out.
Thank you!!!