HI - looks like maybe the fieldmap inputs are not setup correctly? Cheers.
> On 17 Jul 2018, at 12:19, Hawasli, Ammar <[email protected]> wrote: > > Hello All, > > I am having a bug with my Gradient Distortion Unwarp process in prefreesurfer > and wanted to reach out for ideas. > > This is what is shows: > > START: GradientDistortionUnwarp > gradunwarp-INFO: Parsing > /mnt/md126p2/Ubuntu/home/functionalspinelab/NecessaryDownloads/HCPpipelines-master/coeff_AS82_Prisma.grad > for harmonics coeffs > gradunwarp-INFO: Evaluating spherical harmonics > gradunwarp-INFO: on a 60^3 grid > gradunwarp-INFO: with extents -300.0mm to 300.0mm > gradunwarp-INFO: along x... > gradunwarp-INFO: along y... > gradunwarp-INFO: along z... > gradunwarp-INFO: Evaluating the jacobian multiplier > gradunwarp-INFO: Unwarping slice by slice > . . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . > . . 40 . . . . . . . . . 50 . . . . . . . . . 60 . . . . . . . . . 70 . . . . > . . . . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 > . . . . . . . . . 120 . . . . . . . . . 130 . . . . . . . . . 140 . . . . . . > . . . 150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180 . > . . . . . . . . 190 . . . . . . . . . 200 . . . . . . . . . 210 . . . . . . . > . . 220 . . . . . . . . . 230 . . . . . . . . . 240 . . . . . . . . . 250 . . > . . . . . . . 260 . . . . . . . . . 270 . . . . . . . . . 280 . . . . . . . . > . 290 . . . . . . . . . 300 . . . . . . . . . 310 . . . . . . . . . 320 > gradunwarp-INFO: Writing output to trilinear.nii.gz > > END: GradientDistortionUnwarp > Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: Not Averaging T2w > Images > Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: ONLY ONE AVERAGE > FOUND: COPYING > Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: Aligning T2w image > to 0.7mm MNI T2wTemplate to create native volume space > Mon Jul 16 15:21:59 CDT 2018 - PreFreeSurferPipeline.sh: mkdir -p > /mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/ACPCAlignment > > START: ACPCAlignment > Final FOV is: > 0.000000 208.000000 0.000000 300.000000 78.000000 188.000000 > > > END: ACPCAlignment > Mon Jul 16 15:23:03 CDT 2018 - PreFreeSurferPipeline.sh: Performing Brain > Extraction using FNIRT-based Masking > Mon Jul 16 15:23:03 CDT 2018 - PreFreeSurferPipeline.sh: mkdir -p > /mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/BrainExtraction_FNIRTbased > > START: BrainExtraction_FNIRT > > END: BrainExtraction_FNIRT > Mon Jul 16 15:29:28 CDT 2018 - PreFreeSurferPipeline.sh: Performing TOPUP > Readout Distortion Correction > Mon Jul 16 15:29:28 CDT 2018 - PreFreeSurferPipeline.sh: mkdir -p > /mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/T2wToT1wDistortionCorrectAndReg > > START: T2WToT1wDistortionCorrectAndReg.sh > Mon Jul 16 15:29:30 CDT 2018 - TopupPreprocessingAll.sh: START: Topup Field > Map Generation and Gradient Unwarping > ERROR: Could not open file > ERROR: Could not open file > ERROR: Could not open file > ERROR: Could not open file > > START: GradientDistortionUnwarp > Cannot open volume > /mnt/md126p2/Ubuntu/home/functionalspinelab/Data/mystudy/CON-015/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/PhaseOne > for reading! > > ____________________ > > > I am using a Prisma and have the new gradunwarp installed which has the bug > fix for global, siemens_cas value. I also obviously have my coefficient file > referenced normally. > > Any ideas? > > Thanks > Ammar > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > _______________________________________________ > HCP-Users mailing list > [email protected] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, WIN (FMRIB) Oxford FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected] http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
