I'm not sure what could have gone wrong in the script, but as you may have guessed, that error means the input surface to -surface-apply-warpfield is too large for the specified warpfield volume, and thus some vertices would have undefined coordinates if it proceeded with the transformation.
Tim On Wed, Jan 6, 2016 at 4:47 AM, Barbara Kreilkamp <bakk....@googlemail.com> wrote: > Dear HCP experts, > > Thank you for all your help so far. > Unfortunately I am running into an error in PostFreeSurferPipelineBatch.sh > I wonder if you could please help me solve this issue? Other participants > with the same data have run without any issues, and the > FreeSurferPipelineBatch.sh completed without any issues as well. > > Thank you, > Best wishes, > Barbara > > ./PostFreeSurferPipelineBatch.sh > > This script must be SOURCED to correctly setup the environment prior to > running any of the other HCP scripts contained here > > > C10 > > About to use fsl_sub to queue or run > /Users/projects/Pipelines/PostFreeSurfer/PostFreeSurferPipeline.sh > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to > 'CTX-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to > 'CTX-RH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to > 'WM-LH-UNKNOWN_1' > > > > WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to > 'WM-RH-UNKNOWN_1' > > > > While running: > > /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command > -surface-apply-warpfield > /Users/projects/Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii > /Users/projects/Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz > /Users/projects/Pipelines_ExampleData/C10/MNINonLinear/Native/C10.L.white.native.surf.gii > -fnirt > /Users/projects/Pipelines_ExampleData/C10/MNINonLinear/xfms/acpc_dc2standard.nii.gz > > > ERROR: surface exceeds the bounding box of the warpfield > > > set -- --path=/Users/projects/Pipelines_ExampleData --subject=C10 > > --surfatlasdir=/Users/projects/Pipelines/global/templates/standard_mesh_atlases > > --grayordinatesdir=/Users/projects/Pipelines/global/templates/91282_Greyordinates > --grayordinatesres=2 --hiresmesh=164 --lowresmesh=32 > > --subcortgraylabels=/Users/projects/Pipelines/global/config/FreeSurferSubcorticalLabelTableLut.txt > > --freesurferlabels=/Users/projects/Pipelines/global/config/FreeSurferAllLut.txt > > --refmyelinmaps=/Users/projects/Pipelines/global/templates/standard_mesh_atlases/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii > --regname=FS --printcom= > > . /Users/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh > > 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