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Dear Matt,
Thank you, I found the brain size parameter, but do you think it is okay
to tweak this, when I leave it at the default value for all the other
subjects (which ran through fine by the way, 58 participants were fine
for the whole myelin pipeline, just 1 patient and 1 control failed in
our dataset, potentially as you pointed out in the acpc-alignment step.
Thank you,
Best wishes,
Barbara
On 15/01/2016 03:08, Glasser, Matthew wrote:
Maybe post your PreFreeSurfer pipeline launch variables.
Peace,
Matt.
From: Barbara Kreilkamp <[email protected]
<mailto:[email protected]>>
Date: Thursday, January 14, 2016 at 6:11 AM
To: Matt Glasser <[email protected] <mailto:[email protected]>>
Cc: "Van Essen, David" <[email protected]
<mailto:[email protected]>>, Timothy Coalson <[email protected]
<mailto:[email protected]>>, "[email protected]
<mailto:[email protected]>" <[email protected]
<mailto:[email protected]>>
Subject: Re: [HCP-Users] ERROR: surface exceeds the bounding box of
the warpfield
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 <[email protected]
<mailto:[email protected]>> wrote:
Indeed sorry Barbara!
Matt.
From: David Van Essen <[email protected] <mailto:[email protected]>>
Date: Tuesday, January 12, 2016 at 11:27 PM
To: Matt Glasser <[email protected] <mailto:[email protected]>>
Cc: Timothy Coalson <[email protected] <mailto:[email protected]>>,
Barbara Kreilkamp <[email protected]
<mailto:[email protected]>>, "[email protected]
<mailto:[email protected]>"
<[email protected]
<mailto:[email protected]>>
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
<[email protected] <mailto:[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
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
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taking of any action in reliance on the contents of this
information is strictly prohibited. If you have received this
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Healthcare Information or other information of a sensitive nature. If
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