Awesome! Thank you all for the help. And for getting back to me so quickly!
Cheers, -Garren On Mon, Jan 29, 2018 at 5:37 PM, Glasser, Matthew <[email protected]> wrote: > 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]> > Date: Monday, January 29, 2018 at 5:36 PM > To: "Elam, Jennifer" <[email protected]> > Cc: Matt Glasser <[email protected]>, "[email protected]" < > [email protected]>, "Coalson, Timothy" <[email protected]>, > "Harwell, John" <[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]> 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 >> [email protected] >> www.humanconnectome.org >> >> ------------------------------ >> *From:* Glasser, Matthew >> *Sent:* Monday, January 29, 2018 5:19:28 PM >> *To:* Garren Gaut; [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]> >> Date: Monday, January 29, 2018 at 5:16 PM >> To: Matt Glasser <[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]> >> wrote: >> >> You have save a scene in workbench after you set everything up how you >> want it. >> >> Peace, >> >> Matt. >> >> From: Garren Gaut <[email protected]> >> Date: Monday, January 29, 2018 at 5:11 PM >> To: Matt Glasser <[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]> >> 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]> on behalf of Garren Gaut < >> [email protected]> >> Date: Monday, January 29, 2018 at 4:45 PM >> To: "[email protected]" <[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 <(949)%20533-4612>[email protected] >> >> _______________________________________________ >> HCP-Users mailing list >> [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 <(949)%20533-4612>[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 <(949)%20533-4612>[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 <(949)%20533-4612>[email protected] > > -- Garren Gaut Department of Cognitive Sciences University of California, Irvine 2279 Social & Behavioral Sciences Gateway Building Irvine, CA 92697-5100 (949)[email protected] _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
