Yes that is what I am suggesting you do. If you want to iterate over files, you would have to use sed and find and replace in the scene file.
Peace, Matt. From: Garren Gaut <[email protected]<mailto:[email protected]>> Date: Monday, January 29, 2018 at 5:36 PM To: "Elam, Jennifer" <[email protected]<mailto:[email protected]>> Cc: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "Coalson, Timothy" <[email protected]<mailto:[email protected]>>, "Harwell, John" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Workbench: save images using the command line 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 <[email protected]<mailto:[email protected]>> 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<tel:314-362-9387> [email protected]<mailto:[email protected]> www.humanconnectome.org<http://www.humanconnectome.org/> ________________________________ From: Glasser, Matthew Sent: Monday, January 29, 2018 5:19:28 PM To: Garren Gaut; [email protected]<mailto:[email protected]> 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 <[email protected]<mailto:[email protected]>> Date: Monday, January 29, 2018 at 5:16 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: You have save a scene in workbench after you set everything up how you want it. Peace, Matt. From: Garren Gaut <[email protected]<mailto:[email protected]>> Date: Monday, January 29, 2018 at 5:11 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> wrote: wb_command -show-scene is used for this purpose. The development version allows you to increment by map index. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Garren Gaut <[email protected]<mailto:[email protected]>> Date: Monday, January 29, 2018 at 4:45 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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<tel:(949)%20533-4612>[email protected]<mailto:[email protected]> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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<tel:(949)%20533-4612>[email protected]<mailto:[email protected]> -- Garren Gaut Department of Cognitive Sciences University of California, Irvine 2279 Social & Behavioral Sciences Gateway Building Irvine, CA 92697-5100 (949)533-4612<tel:(949)%20533-4612>[email protected]<mailto:[email protected]> -- Garren Gaut Department of Cognitive Sciences University of California, Irvine 2279 Social & Behavioral Sciences Gateway Building Irvine, CA 92697-5100 (949)533-4612 [email protected]<mailto:[email protected]> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
