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
> 
> 
>  
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