[HCP-Users] problem with FreeSurfer2CaretConvertAndRegisterNonlinear
Dear HCP-users list I am new to the HCP pipeline and I'm experiencing a problem while running PostFreeSurferPipelineBatch.s on Mac-Os. I get the following error message: While running: /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -surface-distortion /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.sphere.native.surf.gii /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.sphere.reg.reg_LR.native.surf.gii /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.Strain_FS.native.shape.gii -local-affine-method ERROR: Unexpected parameter: -local-affine-method Can anybody help? Thanks and best wishes Mara ___ This email has been scanned by MessageLabs' Email Security System on behalf of the Brighton & Sussex Medical School. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] problem with FreeSurfer2CaretConvertAndRegisterNonlinear
Hi Mara, Tim posted about this about a month ago or so. I'm copying/pasting his response for your reference: That is a new option that is not yet in a released version of workbench, and was probably not intended to be pushed to the pipelines repository. You can use github to find the version before that line was added, and use that instead. Alternatively, you can probably just comment out that line and any that reference the generated file, it is probably for visualization purposes only. Finally, you could use a development version of workbench which does have that option. The dev_latest versions here probably have it: http://brainvis.wustl.edu/workbench/ However, please do not make any scene files with any dev_latest version of wb_view, because when we change things in the GUI during development, the scene files may become incompatible. Tim On Thu, Nov 2, 2017 at 10:45 AM, Mara Cercignani wrote: > Dear HCP-users list > > I am new to the HCP pipeline and I'm experiencing a problem while running > PostFreeSurferPipelineBatch.s on Mac-Os. > > I get the following error message: > > While running: > > /Applications/workbench/bin_macosx64/../macosx64_apps/wb_ > command.app/Contents/MacOS/wb_command -surface-distortion > /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.sphere.native.surf.gii > /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1. > L.sphere.reg.reg_LR.native.surf.gii /Users/MC/subjects/Subject1/ > MNINonLinear/Native/Subject1.L.Strain_FS.native.shape.gii > -local-affine-method > > > ERROR: Unexpected parameter: -local-affine-method > > > Can anybody help? > > > Thanks and best wishes > > Mara > > ___ > This email has been scanned by MessageLabs' Email Security System > on behalf of the Brighton & Sussex Medical School. For more information > see: > https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > -- Niels Bergsland Integration Director / Research Assistant Professor of Neurology Buffalo Neuroimaging Analysis Center / University at Buffalo 100 High St. Buffalo NY 14203 npbergsl...@bnac.net ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] problem with FreeSurfer2CaretConvertAndRegisterNonlinear
If you search the list you will see a response to this. We hope to get out a new official version of Connectome Workbench soon so that folks won’t run into this, but you can either install a development version or comment out that line for now/ Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Mara Cercignani mailto:m.cercign...@bsms.ac.uk>> Date: Thursday, November 2, 2017 at 4:45 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] problem with FreeSurfer2CaretConvertAndRegisterNonlinear Dear HCP-users list I am new to the HCP pipeline and I'm experiencing a problem while running PostFreeSurferPipelineBatch.s on Mac-Os. I get the following error message: While running: /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -surface-distortion /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.sphere.native.surf.gii /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.sphere.reg.reg_LR.native.surf.gii /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.Strain_FS.native.shape.gii -local-affine-method ERROR: Unexpected parameter: -local-affine-method Can anybody help? Thanks and best wishes Mara ___ This email has been scanned by MessageLabs' Email Security System on behalf of the Brighton & Sussex Medical School. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] problem with FreeSurfer2CaretConvertAndRegisterNonlinear
Thank you both - I've manage to run it to the end following your advice Best wishes From: Glasser, Matthew [glass...@wustl.edu] Sent: 03 November 2017 00:21 To: Mara Cercignani; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] problem with FreeSurfer2CaretConvertAndRegisterNonlinear If you search the list you will see a response to this. We hope to get out a new official version of Connectome Workbench soon so that folks won’t run into this, but you can either install a development version or comment out that line for now/ Peace, Matt. From: > on behalf of Mara Cercignani > Date: Thursday, November 2, 2017 at 4:45 AM To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] problem with FreeSurfer2CaretConvertAndRegisterNonlinear Dear HCP-users list I am new to the HCP pipeline and I'm experiencing a problem while running PostFreeSurferPipelineBatch.s on Mac-Os. I get the following error message: While running: /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -surface-distortion /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.sphere.native.surf.gii /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.sphere.reg.reg_LR.native.surf.gii /Users/MC/subjects/Subject1/MNINonLinear/Native/Subject1.L.Strain_FS.native.shape.gii -local-affine-method ERROR: Unexpected parameter: -local-affine-method Can anybody help? Thanks and best wishes Mara ___ This email has been scanned by MessageLabs' Email Security System on behalf of the Brighton & Sussex Medical School. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ This email has been scanned by MessageLabs' Email Security System on behalf of the Brighton & Sussex Medical School. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___ This email has been scanned by MessageLabs' Email Security System on behalf of the Brighton & Sussex Medical School. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
