Hey All, I think I figured out why the save scene process is inefficient for me. My cifti files have 1 map per file, which would mean saving a scene file for each cifti file. It seems like the way workbench was designed (which i missed) is to put multiple maps in one file, save only one scene, and then use -show-scene to iterate over maps to save? If that is the general process then I should be fine.
Cheers, -Garren 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 > > -- Garren Gaut Department of Cognitive Sciences University of California, Irvine 2279 Social & Behavioral Sciences Gateway Building Irvine, CA 92697-5100 (949)533-4612gbiu...@gmail.com _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
