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users > RE: eddy current correction error
Nov 13, 2018 02:11 PM | Therese Sjoholm
RE: eddy current correction error
Hello,
If I first create the b0_S1_fwd_2.xform folder it seems like the eddy current correction step is not run. The complete command line is then:
thesj165@RUD-L11331 ~
$ cmtk correct_dwi_distortion /cygdrive/c/Users/thesj165/Documents/dwi/scans/pil ot/UPMR0044_Pilot1/cmtk_dc/test /cygdrive/c/Users/thesj165/Documents/dwi/scans/p ilot/UPMR0044_Pilot1/raw/DWI_STIR_2b_PA_1/S1_rev_1.nii.gz /cygdrive/c/Users/thes j165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/raw/DWI_SSRF_S1/S1_fwd_1.nii.gz / cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/raw/DWI_SSRF _S1/S1_fwd_2.nii.gz
which: no lockfile in (/usr/local/bin:/usr/bin:/cygdrive/c/WINDOWS/system32:/cyg drive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/WINDOWS/System32/W indowsPowerShell/v1.0:/cygdrive/c/Program Files/MATLAB/R2018b/bin:/cygdrive/c/Pr ogram Files/MATLAB/R2018a/bin:/cygdrive/c/Program Files/dotnet:/cygdrive/c/WINDO WS/System32/OpenSSH:/cygdrive/c/Users/thesj165/AppData/Local/Microsoft/WindowsAp ps:/cygdrive/c/Program Files/elastix_v4.8:/cygdrive/c/Users/thesj165/AppData/Loc al/Continuum/anaconda3:/cygdrive/c/Users/thesj165/AppData/Local/Continuum/anacon da3/Scripts:/usr/lib)
========================================================================
CREATE /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/cmtk _dc/test/dfield_fwd.nrrd
========================================================================
Computing deformation...
========================================================================
CREATE /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/cmtk_dc/test/S1_fwd_2.nii.gz
========================================================================
Unwarping /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/raw/DWI_SSRF_S1/S1_fwd_2.nii.gz
The file/directory /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/cmtk_dc/test/eddy/b0_S1_fwd_2.xform does not seem to be in a supported transformation format
Best,
Therese
If I first create the b0_S1_fwd_2.xform folder it seems like the eddy current correction step is not run. The complete command line is then:
thesj165@RUD-L11331 ~
$ cmtk correct_dwi_distortion /cygdrive/c/Users/thesj165/Documents/dwi/scans/pil ot/UPMR0044_Pilot1/cmtk_dc/test /cygdrive/c/Users/thesj165/Documents/dwi/scans/p ilot/UPMR0044_Pilot1/raw/DWI_STIR_2b_PA_1/S1_rev_1.nii.gz /cygdrive/c/Users/thes j165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/raw/DWI_SSRF_S1/S1_fwd_1.nii.gz / cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/raw/DWI_SSRF _S1/S1_fwd_2.nii.gz
which: no lockfile in (/usr/local/bin:/usr/bin:/cygdrive/c/WINDOWS/system32:/cyg drive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/WINDOWS/System32/W indowsPowerShell/v1.0:/cygdrive/c/Program Files/MATLAB/R2018b/bin:/cygdrive/c/Pr ogram Files/MATLAB/R2018a/bin:/cygdrive/c/Program Files/dotnet:/cygdrive/c/WINDO WS/System32/OpenSSH:/cygdrive/c/Users/thesj165/AppData/Local/Microsoft/WindowsAp ps:/cygdrive/c/Program Files/elastix_v4.8:/cygdrive/c/Users/thesj165/AppData/Loc al/Continuum/anaconda3:/cygdrive/c/Users/thesj165/AppData/Local/Continuum/anacon da3/Scripts:/usr/lib)
========================================================================
CREATE /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/cmtk _dc/test/dfield_fwd.nrrd
========================================================================
Computing deformation...
========================================================================
CREATE /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/cmtk_dc/test/S1_fwd_2.nii.gz
========================================================================
Unwarping /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/raw/DWI_SSRF_S1/S1_fwd_2.nii.gz
The file/directory /cygdrive/c/Users/thesj165/Documents/dwi/scans/pilot/UPMR0044_Pilot1/cmtk_dc/test/eddy/b0_S1_fwd_2.xform does not seem to be in a supported transformation format
Best,
Therese
Threaded View
Title | Author | Date |
---|---|---|
Therese Sjoholm | Oct 31, 2018 | |
Torsten Rohlfing | Nov 2, 2018 | |
Therese Sjoholm | Nov 5, 2018 | |
Torsten Rohlfing | Nov 10, 2018 | |
Therese Sjoholm | Nov 13, 2018 | |
Torsten Rohlfing | Nov 15, 2018 | |
Therese Sjoholm | Nov 15, 2018 | |