After some brief internal discussion, we think it would be fastest to figure out what went wrong if we had a look at the files. To start with, can you zip up the following 3 files:
Pipelines_ExampleData/C10/T1w/Native/C10.L.white.native.surf.gii Pipelines_ExampleData/C10/MNINonLinear/xfms/standard2acpc_dc.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz And upload them here: http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson <tsc...@mst.edu> wrote: > 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 >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
