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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