Thank you very much for looking into it. I have now uploaded the files. Thank you, Best wishes, Barbara
On Wed, Jan 6, 2016 at 11:19 PM, Timothy Coalson <tsc...@mst.edu> wrote: > 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
