It won’t create any biases, it just might help you get the acpc step to work on the two subjects it hasn’t.
Peace, Matt. From: Barbara Kreilkamp <bakk....@googlemail.com<mailto:bakk....@googlemail.com>> Date: Friday, January 15, 2016 at 9:46 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Van Essen, David" <vanes...@wustl.edu<mailto:vanes...@wustl.edu>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "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 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 <bakk....@googlemail.com<mailto:bakk....@googlemail.com>> Date: Thursday, January 14, 2016 at 6:11 AM To: Matt Glasser <<mailto:glass...@wustl.edu>glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Van Essen, David" <vanes...@wustl.edu<mailto:vanes...@wustl.edu>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "<mailto:hcp-users@humanconnectome.org>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 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<mailto:glass...@wustl.edu>> wrote: Indeed sorry Barbara! Matt. From: David Van Essen <vanes...@wustl.edu<mailto:vanes...@wustl.edu>> Date: Tuesday, January 12, 2016 at 11:27 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Barbara Kreilkamp <bakk....@googlemail.com<mailto:bakk....@googlemail.com>>, "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 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 <<mailto:glass...@wustl.edu>glass...@wustl.edu<mailto: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: <<mailto:hcp-users-boun...@humanconnectome.org>hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <<mailto:tsc...@mst.edu>tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Friday, January 8, 2016 at 6:42 PM To: Barbara Kreilkamp <<mailto:bakk....@googlemail.com>bakk....@googlemail.com<mailto:bakk....@googlemail.com>> Cc: "<mailto:hcp-users@humanconnectome.org>hcp-users@humanconnectome.org<mailto: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 <<mailto:bakk....@googlemail.com>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 <<mailto:bakk....@googlemail.com>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 <<mailto:tsc...@mst.edu>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>http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson <<mailto:tsc...@mst.edu>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 <<mailto:bakk....@googlemail.com>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 <mailto:HCP-Users@humanconnectome.org>HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list <mailto:HCP-Users@humanconnectome.org>HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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