The error you are getting is likely because you specified the wrong kind of file to an argument of the command (metric when it expected a surface).
To expand on what Matt said, in order to find a problem of this nature (or really figure out any problem encountered with wb_command), we need to know the full command line that was run that produced this error, not just the error message. The full command line should be part of the output wb_command gives when it encounters an error, in order to make this reporting easier. Tim On Tue, Jan 10, 2017 at 12:34 PM, Leah Moreno <[email protected]> wrote: > 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 <(314)%20747-6173> > > 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/FreeSurfer2CaretConvertAndRegi > sterNonlinear.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. 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