Dear Matt, David and Tim, Thanks for looking into it, I've got the 1mm templates with their correct paths, however I am unsure of how to test performance implementing these as "down sampled, and brain mask" as well as where to change the brain size parameter.
Would you guide me on this please? Thank you, Best wishes, Barbara On Wed, Jan 13, 2016 at 11:07 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > Indeed sorry Barbara! > > Matt. > > From: David Van Essen <vanes...@wustl.edu> > Date: Tuesday, January 12, 2016 at 11:27 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: Timothy Coalson <tsc...@mst.edu>, Barbara Kreilkamp < > bakk....@googlemail.com>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > > Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of the > warpfield > > Thanks for the suggestions, Matt, which are excellent even though > accidentally addressed to the wrong gender - said your mentor, > (s)heepishly. > > David :<) > > On Jan 12, 2016, at 10:23 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > 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> on behalf of Timothy > Coalson <tsc...@mst.edu> > Date: Friday, January 8, 2016 at 6:42 PM > To: Barbara Kreilkamp <bakk....@googlemail.com> > Cc: "hcp-users@humanconnectome.org" <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 > > 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> 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 >>>>>> >>>>> >>>>> >>>> >>> >> > 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If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
