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 <[email protected]> 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: <[email protected] > <mailto:[email protected]>> on behalf of Timothy Coalson > <[email protected] <mailto:[email protected]>> > Date: Friday, January 8, 2016 at 6:42 PM > To: Barbara Kreilkamp <[email protected] > <mailto:[email protected]>> > Cc: "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>> > 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 <[email protected] > <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >>> <mailto:[email protected]>> 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 >>>> <http://brainvis.wustl.edu/cgi-bin/upload.cgi> >>>> >>>> Tim >>>> >>>> >>>> On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson <[email protected] >>>> <mailto:[email protected]>> 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 >>>>> <[email protected] <mailto:[email protected]>> 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 >>>>>> [email protected] <mailto:[email protected]> >>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >>>> >>> >> > > _______________________________________________ > HCP-Users mailing list > [email protected] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <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. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
