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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
