Thank you, Matt. I want to do what you suggested.
Could I map my processed resting-data to individual surfaces and create ‘dtseries.nii’ files and run FC analyses on these files? Also, when I am creating individual surfaces from Freesurfer to Workbench I still get the same error “Number of data arrays MUST be two in a SurfaceFile”. I am following these steps: mris_convert white and pial to surf.gii wb_command -set-structure on these new files I am not doing: wb_command -surface-apply-affine (I do not have ‘mri/c_ras.mat’) wb_command -surface-apply-warpfield wb_command -surface-average to create midthickness wb_command -set-structure and finally wb_command -surface-generate-inflated But when I map my FCmaps on this final midthickness or inflated surfaces I am getting that error of “Number of data arrays MUST be two in a SurfaceFile”. I am not converting well my files from FS to workbench. Thank you very much ********************************** Leah Moreno, PhD Associate Research Scientist Division of Experimental Therapeutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (646) 774-5404 email: [email protected] email: [email protected] From: "Glasser, Matthew" <[email protected]> Date: Tuesday, January 10, 2017 at 12:52 PM To: Leah Moreno <[email protected]>, "Harms, Michael" <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench All you have to do is not smooth your data in the volume, not average it across subjects in the volume, and map data from individual volumes to individual surfaces. Then you can average across subjects on the surface using a folding-based surface registration. Just doing these things dramatically improves your ability to know where you are in the cerebral cortex. Peace, Matt. From: Leah Moreno <[email protected]> Date: Tuesday, January 10, 2017 at 11:40 AM To: "Harms, Michael" <[email protected]>, Matt Glasser <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench I know, Michael. Thank you. Unfortunately, this dataset was not collected following HCP requirements and I only have resting-state and MPRAGE data. ********************************** Leah Moreno, PhD Associate Research Scientist Division of Experimental Therapeutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (646) 774-5404 email: [email protected] email: [email protected] From: "Harms, Michael" <[email protected]> Date: Tuesday, January 10, 2017 at 10:58 AM To: Leah Moreno <[email protected]>, "Glasser, Matthew" <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench Hi Leah, Just an aside: If you are projecting FC maps (derived inherently in volume space) to the surface for visualization you won’t have the benefits of a true surface-based analysis. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected] From: <[email protected]> on behalf of Leah Moreno <[email protected]> Date: Sunday, January 8, 2017 at 12:19 PM To: "Glasser, Matthew" <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] Freesurfer and workbench Matt, following more carefully the link you sent me I realized I was not doing all the steps detailed in there. Thank you for your help. -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 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
