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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