I have done the following steps: 1. mris_convert to cretae white and pial surfaces from freesurfer
2. Create midthickness by averaging white and pial surfaces with wb_command -surface-average 3. create inflated and very inflated with wb_command -surface-generate-inflated with -iterations-scale 0.75 4. Then I maped the FCmap to the midthickness using wb_command -volume-to-surface-mapping –enclosing Thank you, -L From: "Glasser, Matthew" <[email protected]> Date: Sunday, January 8, 2017 at 11:45 AM To: Leah Moreno <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench I would need to know the exact commands you used in the process of converting the surfaces and doing the volume to surface mapping. Peace, Matt. From: Leah Moreno <[email protected]> Date: Sunday, January 8, 2017 at 11:43 AM To: Matt Glasser <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench Once cretaed midthickness.surf.gii I am mapping the volume FCmap with wb_command -volume-to-surface-mapping but getting this error: “Number of data arrays MUST be two in a SurfaceFile”. What am I doing wrong? Thank you, -L From: "Glasser, Matthew" <[email protected]> Date: Sunday, January 8, 2017 at 11:20 AM To: Leah Moreno <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench Right. Matt. From: Leah Moreno <[email protected]> Date: Sunday, January 8, 2017 at 11:18 AM To: Matt Glasser <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench Could I reduce the entire code to these main lines? mris_convert Create midthickness by averaging white and pial surfaces with wb_command -surface-average And create inflated and very inflated with wb_command -surface-generate-inflated with -iterations-scale 0.75 Thank you, -L From: "Glasser, Matthew" <[email protected]> Date: Sunday, January 8, 2017 at 10:43 AM To: Leah Moreno <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench All this code is available here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh Particularly starting on Line 117. Matt. From: Leah Moreno <[email protected]> Date: Sunday, January 8, 2017 at 10:33 AM To: Matt Glasser <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench Great, thank you. And how do you generate midthickness and inflated surfaces from white, pial, and spherical surfaces once they are converted to .surf.gii? -L From: "Glasser, Matthew" <[email protected]> Date: Sunday, January 8, 2017 at 10:27 AM To: Leah Moreno <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench We typically convert the white, pial, and spherical surfaces from FreeSurfer with mris_convert. We then generate midthickness and inflated surfaces which are the main surfaces used for visualization. Peace, Matt. From: <[email protected]> on behalf of Leah Moreno <[email protected]> Date: Sunday, January 8, 2017 at 10:20 AM To: "[email protected]" <[email protected]> Subject: [HCP-Users] Freesurfer and workbench Dear users, An easy question, which is the surface file from Freesurfer I need to convert to .surf.gii format in order to use workbench instead of Freesurfer to create rois and visualize subject FC maps in subject surface space? Thank you, -L _______________________________________________ HCP-Users mailing list [email protected] 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. 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. 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. 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
