No, scene files are highly GUI-centric, taking captures of what is in a scene is somewhat secondary. The number of display options for files (and when we add new display features) would make it very cumbersome to make and maintain a command to do the equivalent without the GUI.
You can set up a scene once, save it, and then use text replacement commands to change it for different subjects or overlays, which may be closer to what you want. Tim On Mon, Jan 29, 2018 at 5:31 PM, Elam, Jennifer <e...@wustl.edu> wrote: > I don't believe there is currently a way to create a scene file outside of > the workbench GUI because several pieces of data that are saved in scene > files (e.g. what files are loaded, layer settings, structure orientation, > zoom level, panning, etc.) are set within the GUI. CC'ing Tim and John in > case they know of a way to do this. > > > Best, > > Jenn > > > Jennifer Elam, Ph.D. > Scientific Outreach, Human Connectome Project > Washington University School of Medicine > Department of Neuroscience, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > e...@wustl.edu > www.humanconnectome.org > > ------------------------------ > *From:* Glasser, Matthew > *Sent:* Monday, January 29, 2018 5:19:28 PM > *To:* Garren Gaut; hcp-users@humanconnectome.org > *Cc:* Elam, Jennifer > > *Subject:* Re: [HCP-Users] Workbench: save images using the command line > > Perhaps Jenn has some text about scenes you can read. The scene saves the > exact state of workbench. You can then export pictures using the command I > mentioned below. The development version allows you to iterate through > multiple maps. > > Peace, > > Matt. > > From: Garren Gaut <gbiu...@gmail.com> > Date: Monday, January 29, 2018 at 5:16 PM > To: Matt Glasser <glass...@wustl.edu> > Subject: Re: [HCP-Users] Workbench: save images using the command line > > Is there a way to save a scene without using the workbench GUI? > > On Mon, Jan 29, 2018 at 5:14 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > > You have save a scene in workbench after you set everything up how you > want it. > > Peace, > > Matt. > > From: Garren Gaut <gbiu...@gmail.com> > Date: Monday, January 29, 2018 at 5:11 PM > To: Matt Glasser <glass...@wustl.edu> > Subject: Re: [HCP-Users] Workbench: save images using the command line > > Thanks Matt, > > I’m trying out the -show-scene function, but am getting an error. Does the > parameter <scene-file> have to point to a scene-file? And if so, is there > a way to create a scene-file using wb_command? The results files I’m trying > to visualize are in .dscalar.nii format. I’m running the command: > > wb_command -show-scene > files/0bck_minus_baseline_mean_contrast_cohensd_whs26_whmodel1.dscalar.nii 1 > test.png 10 10 -use-window-size > > and am getting the error: > > While running: > /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command > -show-scene > files/0bck_minus_baseline_mean_contrast_cohensd_whs26_whmodel1.dscalar.nii 1 > test.png 10 10 -use-window-size > > ERROR: Parse Error while reading:: error occurred while parsing element, line > number: 1 column number: 1 > > File: 0bck_minus_baseline_mean_contrast_cohensd_whs26_whmodel1.dscalar.nii > Path: /Users/Garren/Dropbox/FMRI/Projects/varianceGLM/ROI2NIfTI/files > > Thanks, > > -Garren > > > On Mon, Jan 29, 2018 at 4:47 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > > wb_command -show-scene is used for this purpose. The development version > allows you to increment by map index. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Garren Gaut < > gbiu...@gmail.com> > Date: Monday, January 29, 2018 at 4:45 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Workbench: save images using the command line > > Hi HCP support, > > I am trying to automate the generation of brain images using workbench. I > have several cifti files containing effect size maps and I would like to > save the maps to images without ever using the workbench GUI. I've written > a script that loads of all my files and sets up the viewing options using > `wb_command`, but I haven't been able to figure out a way to save workbench > images from the command line. Is there a way to use `wb_command` (or some > other tool) to do this? > > Let me know if there is anything I can clarify or provide that you need. I > appreciate the help. > > Thank you! > > -Garren > > -- > > Garren Gaut > Department of Cognitive Sciences > University of California, Irvine > 2279 Social & Behavioral Sciences Gateway Building > Irvine, CA 92697-5100(949)533-4612 <(949)%20533-4612>gbiu...@gmail.com > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > -- > > Garren Gaut > Department of Cognitive Sciences > University of California, Irvine > 2279 Social & Behavioral Sciences Gateway Building > Irvine, CA 92697-5100(949)533-4612 <(949)%20533-4612>gbiu...@gmail.com > > > > > -- > > Garren Gaut > Department of Cognitive Sciences > University of California, Irvine > 2279 Social & Behavioral Sciences Gateway Building > Irvine, CA 92697-5100(949)533-4612 <(949)%20533-4612>gbiu...@gmail.com > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
