They are in the file HCP_Boundig_Box_error Thank you, Best wishes, Barbara On Fri, Jan 8, 2016 at 12:12 PM, Barbara Kreilkamp <bakk....@googlemail.com> wrote:
> 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
