Hi Ammar,

Please post your .bat call to the pipeline script.  Most likely you need to set 
somethings to NONE

Matt.

From: 
<[email protected]<mailto:[email protected]>>
 on behalf of Steve Smith <[email protected]<mailto:[email protected]>>
Date: Tuesday, July 17, 2018 at 11:23 AM
To: "Hawasli, Ammar" <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] GradientDistortionUnwarp error help.

HI - looks like maybe the fieldmap inputs are not setup correctly?
Cheers.


On 17 Jul 2018, at 12:19, Hawasli, Ammar 
<[email protected]<mailto:[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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