Indeed the acpc registration is failing. He might check to be sure he is using the right templates (1mm, correct ones for original, down sampled, and brain mask). He could also try fiddling with the brain size parameter (trying values 10mm larger and smaller than 150mm). The acpc stage is most vulnerable to failure. If it works, usually everything else will after it.
Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Friday, January 8, 2016 at 6:42 PM To: Barbara Kreilkamp <bakk....@googlemail.com<mailto:bakk....@googlemail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield Well, somewhere along the line, volume registration got messed up, and clipped off some cortex, as in the attached capture. We think it might be in the ACPC alignment step, as it has caused some problems before. Could you next zip up the following files so we can take a look, and upload them the same way: Pipelines_ExampleData/C10/T1w/ACPCAlignment (the entire directory) Pipelines_ExampleData/C10/T1w/T1w.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc.nii.gz Tim On Fri, Jan 8, 2016 at 6:15 AM, Barbara Kreilkamp <bakk....@googlemail.com<mailto:bakk....@googlemail.com>> wrote: 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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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