https://www.wiki.anthonycate.org/ 2026-04-19T02:26:11+00:00 https://www.wiki.anthonycate.org/ https://www.wiki.anthonycate.org/lib/exe/fetch.php?media=wiki:logo.png text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:awk_resources&rev=1558555692&do=diff awk programming resources Clean up SPM table .csv files <2016-01-14> Anthony did this for the MathWONC project (see here). Here is the code from cleanup_awk_linux.sh: # cleanup_awk.sh # bash script to run awk commands # For removing lines from spm table .csv files # Removes lines with "Unidentified" or any other simple criterion # # Use: $ bash cleanup_awk.sh spm_table_file_name.csv # # 2016.01.14 by adc # Remove unwanted columns # # $1 is the variable that holds the first input argument … text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:bash_resources&rev=1558555692&do=diff bash Resources bash variables <2014.6.24> List names, values and types of all variables Useful on the command line, to see what you're working with: declare -p ---------- bash command prompt customization <2016-01-27> Show cwd basename, not entire absolute path text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:cortical_anatomy&rev=1558555692&do=diff Resources for learning to identify cortical landmarks For the lobes: <http://sciencenetlinks.com/tools/3d-brain/> For the details: <http://culhamlab.ssc.uwo.ca/fmri4newbies/PrimeronCorticalSulci.html> <http://sumsdb.wustl.edu/sums/humanpalsmore.do> <http://sumsdb.wustl.edu/sums/index.jsp> <http://www.med.harvard.edu/AANLIB/home.html> <https://www.msu.edu/~brains/brains/human/index.html> For the ridiculously fine details: <http://www.cma.mgh.harvard.edu/manuals/parcellation/> … text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:cs_journals&rev=1558555692&do=diff Summaries of guidelines for some CS journals Journals with highest impact factors <http://www.spinellis.gr/blog/20140808/> Computer Science journal rankings <http://www.scimagojr.com/journalrank.php?area=1700> Foundations and Trends in Human-Computer Interaction Desney Tan's study was about 29 pages long. <http://www.nowpublishers.com/HCI> International Journal of Human-Computer Interaction Studies text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:emacs_resources&rev=1558555692&do=diff Emacs Resources Regular expressions (“regexps,” “regexp,” “regex”) Links to helpful pages <http://www.emacswiki.org/emacs/RegularExpression> <https://www.gnu.org/software/emacs/manual/html_node/elisp/Replacing-Match.html> ---------- Recipes Replace single spaces after end of sentence with two spaces in Emacs <2015.6.24> Type the following: [M-x] query-replace-regexp [RET] \. \([A-Z]\) [RET] . \1 [RET] text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:face_datasets&rev=1558555692&do=diff Face image data sets available online. In many cases you will have to email the maintainer for permission and a login, which is painless. * 3d face database software. (n.d.-a). Retrieved March 3, 2014, from <http://pics.stir.ac.uk/ESRC/software.html> * 3d face database software. (n.d.-b). Retrieved from text/html 2023-10-17T19:10:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:firmware_updating_advice&rev=1697569834&do=diff From: https://askubuntu.com/questions/1451506/how-to-make-ubuntu-22-04-work-with-a-radeon-rx-7900-xtx/1451852#1451852 1. Install the latest OEM kernel available by running the command: sudo apt install linux-oem-22.04c 2. Download and install the latest kernel firmware from here by running these commands: wget https://git.kernel.org/pub/scm/linux/kernel/git/firmware/linux-firmware.git/snapshot/linux-firmware-20230919.tar.gz tar -xf linux-firmware-20230919.tar.gz sudo cp linux-firmware-2… text/html 2023-10-15T15:10:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:git_software&rev=1697382656&do=diff Git software methods Quinn's git tutorial text/html 2023-10-25T18:07:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:glxgears_output&rev=1698257242&do=diff glxgears output Running synchronized to the vertical refresh. The framerate should be approximately the same as the monitor refresh rate. 657 frames in 5.0 seconds = 131.242 FPS X connection to :0.0 broken (explicit kill or server shutdown). GL_RENDERER = AMD Radeon RX 580 2048SP (polaris10, LLVM 16.0.6, DRM 3.54, 6.2.0-34-generic) GL_VERSION = 4.6 (Compatibility Profile) Mesa 23.2.0-devel GL_VENDOR = AMD GL_EXTENSIONS = GL_ARB_multisample GL_EXT_abgr GL_EXT_bgra GL_EXT_blend_colo… text/html 2023-10-25T18:21:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:glxinfo_output&rev=1698258114&do=diff glxinfo output glxinfo -v Ouput: name of display: :0.0 display: :0 screen: 0 direct rendering: Yes server glx vendor string: SGI server glx version string: 1.4 server glx extensions: GLX_ARB_context_flush_control, GLX_ARB_create_context, GLX_ARB_create_context_no_error, GLX_ARB_create_context_profile, GLX_ARB_create_context_robustness, GLX_ARB_fbconfig_float, GLX_ARB_framebuffer_sRGB, GLX_ARB_multisample, GLX_EXT_create_context_es2_profile, GLX_EXT_create_context_e… text/html 2024-02-26T15:09:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:grogu_glxgears&rev=1708960172&do=diff grogu complete glxgears -info output GL_RENDERER = AMD Radeon RX 580 2048SP (polaris10, LLVM 15.0.7, DRM 3.54, 6.5.0-21-generic) GL_VERSION = 4.6 (Compatibility Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 GL_VENDOR = AMD GL_EXTENSIONS = GL_ARB_multisample GL_EXT_abgr GL_EXT_bgra GL_EXT_blend_color GL_EXT_blend_minmax GL_EXT_blend_subtract GL_EXT_copy_texture GL_EXT_subtexture GL_EXT_texture_object GL_EXT_vertex_array GL_EXT_compiled_vertex_array GL_EXT_texture GL_EXT_texture3D GL_IBM_rast… text/html 2024-03-07T15:32:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:grogu_setup&rev=1709825534&do=diff grogu setup Third Try 2024-02-20 In summary, Second Try to install VPixx 3DPixx was doomed by having copied the wrong file to /usr/share/X11/xorg.conf.d/xorg.conf. However, I didn't understand that until part of the way through this here third try. text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:human_subjects_training&rev=1558555692&do=diff VT Human Subjects Protections training Everyone who helps to conduct research in the lab, in any fashion, must complete human subjects protection training. You must complete the online training tutorial before you can be assigned an official role in a research study's IRB protocol. text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:imagemagick_resources&rev=1558555692&do=diff ImageMagick Resources ImageMagick is a set of command line tools that usually comes standard with Linux distributions. <http://www.imagemagick.org/script/index.php> Make thumbnail images of posters from PDF files <2015.6.26> On the Linux/Cygwin/OS X command line: $ convert -thumbnail 300 Cate_Brown_Roldan_SfN_2014_FINAL.pdf outputFileName.png text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:lab_stereo_hardware&rev=1558555692&do=diff Stereo Display Hardware fMRI stereo projection system PROPixx projector: <http://vpixx.com/products/tools-for-vision-sciences/visual-stimulus-displays/propixx/> ---------- Desktop stereo display system Location: “boots” room DATAPixx display driver (blue box): <http://vpixx.com/products/tools-for-vision-sciences/display-drivers/datapixx/> ---------- Vision testing system The Optec 2000 ® screening system: text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:lme&rev=1558555692&do=diff Linear Mixed Effects Regression <2014.2.10> AC's attempts at learning to do this in R. Added package lme4 to R. <http://cran.r-project.org/web/packages/lme4/lme4.pdf> Also added plyr package, because it has a rename() function for renaming columns in a data frame: (<http://www.cookbook-r.com/Manipulating_data/Renaming_columns_in_a_data_frame/>) However, I found it easier to do this: text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:lynda_tutorials&rev=1558555692&do=diff lynda.com Software Tutorials Anyone with a VT login can access video tutorials for a wide range of software at lynda.com <http://lynda.vt.edu/> Tutorials include MATLAB Octave R git xml ssh bash (and other Linux command line and scripting tools) All kinds of internet and web development tools text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:marsbar_software&rev=1558555692&do=diff MarsBar Script Mode text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:matlab_software&rev=1558555692&do=diff MATLAB tutorials To open MATLAB on an Ubuntu Linux computer * Use this keyboard shortcut to open a Linux command line terminal (this is NOT the matlab terminal!): ctrl-alt-t * Type this on the command line (the “&” is optional but handy): text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:mri_top&rev=1558555692&do=diff MRI Scheduling <https://webmail.vtc.vt.edu/> login: cate_lab MRI Scanning Scanner screen dimensions Scanner protocols ---------- Data transfer and storage Get MRI data from scanner Backup scanner data to DVD ---------- Data Analysis Viewing images fMRI preprocessing SPM preprocessing notes fMRI Statistical Analysis Generating SPM reports Overview guide for functional analysis scripts text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:nirs_top&rev=1558555692&do=diff NIRS (Near-Infrared Spectroscopy) NIRx system <http://www.nirx.net/imagers/nirscout> fNIRS_downstate analysis software <http://www.nitrc.org/projects/fnirs_downstate> text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:octave_software&rev=1558555692&do=diff GNU Octave Software Resources Installing Octave packages [These notes are from Anthony's efforts on the Ubuntu 14.04 VirtualBox virtual machine running on his 2015 Macbook Air laptop.] <2016-01-17> Started installing packages on Octave via Octave command line. text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:pdf_document_resources&rev=1558555692&do=diff PDF Document Resources Interleave pages of two versions of lecture slides <2016-01-25> Anthony teaches by distributing a copy of his lectures slides replete with blanks, for students to bring to class, and then presenting the complete version of the slides during lectures. text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:pls_software&rev=1558555692&do=diff Mean Centered: data will be mean centered before being decomposed with singular value decomposition to singular values, singular vectors, etc. Treats the brain as singular values: finds modes in data or values that vary together. Non rotated, Non rotated behavior, non-rotated multiblock: user must have contrasts Mean centered type: choose the kind of mean centering of the data matrix before running Mean Centering task; multiblock pls & non rotated multiblock pls Types 0 – Within each group. R… text/html 2023-10-16T18:51:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:ptb-matlab_installation_messages&rev=1697482269&do=diff 2023-10-16 anthony@grogu:~$ sudo apt install matlab-psychtoolbox-3 Reading package lists... Done Building dependency tree... Done Reading state information... Done The following additional packages will be installed: libgfortran-11-dev libgl1-mesa-glx libjsoncpp25 libopenxr-loader1 matlab-psychtoolbox-3-nonfree matlab-support neurodebian-popularity-contest octave-psychtoolbox-3 popularity-contest psychtoolbox-3-common psychtoolbox-3-lib text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:publishing_resources&rev=1558555692&do=diff Resources for publishing Computer Science journals Summaries of guidelines for some CS journals text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:quinn_git_tutorial&rev=1558555692&do=diff Quinn's git tutorial given to ADC on 2014.3.26 Register for free private github repositories * Cool folks say “repos” * Got message saying I'd hear in about a week Practice creating a remote repo on github text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:r_profile&rev=1558555692&do=diff Customizing startup and shutdown using an Rprofile.site file <2014.3.10> On windows, using the default R gui. Complete text of ADC's Rprofile.site file on Windows Note: here's info saying that the standard R functions for history won't work using native Mac OSX R.App: <http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html> (see section 2.4.10 History) text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:r_software&rev=1558555692&do=diff Lab software notes for R Customizing startup and shutdown lynda.com Several video tutorials, including walk-throughs of common analyses (e.g. multiple regression). lynda.com Software Tutorials text/html 2024-07-01T00:51:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:resources&rev=1719795073&do=diff Lab Procedures ---------- Psychophysics Stereoscopic Displays Stereograms using Psychtoolbox ---------- Publishing Publishing resources Guides and Tutorials ---------- Neuroscience Topics Learning cerebral cortex anatomy Importance of color in face perception Holism, Familiarity and Capgras Crowd sourcing experimental data Retinotopy ---------- Statistics linear mixed effects regression ---------- Programming & Software Science & Math text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:topic_retinotopy_reviews_bib_extended&rev=1558555692&do=diff <html> <html xmlns=“<http://www.w3.org/1999/xhtml>”><head><meta http-equiv=“Content-Type” content=“text/html; charset=UTF-8”><title>Zotero Report</title><link rel=“stylesheet” type=“text/css” href=“Zotero%20Report_retinotopy_reviews_files/detail.css”><link rel= text/html 2019-05-22T20:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:topic_retinotopy&rev=1558555692&do=diff Neuroscience Topics: Retinotopy Bibliography Subtopics from the bibliography Retinotopy: review articles Extended version, including full text URLs and abstracts (This one is in chronological order.) <html> <!DOCTYPE html PUBLIC “-W3CDTD XHTML 1.1EN” “<http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd>”> <html xmlns=“<http://www.w3.org/1999/xhtml>” xml:lang=“en” text/html 2024-01-26T15:21:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:vpixx_setup_first_try&rev=1706282490&do=diff VPixx setup (first try) Checking VPixx functioning after connecting it to PC and CRT for first time 2023-10-05 notes I connected the Datapixx and the CRT monitor to the grogu PC today (and to each other, of course). I also connected the IR emitter. text/html 2024-02-23T22:02:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.wiki.anthonycate.org/doku.php?id=resources:vpixx_setup_second_try&rev=1708725737&do=diff VPixx setup (second try) This is the second try 2024-01-26 I “broke” the display two days ago when trying to fix a package upgrade issue that was stopping the graphics card driver from working, I think. The main error seemed to be that there was a newer version of some package installed, but an older version was needed, so I finally just tried removing everything. Then the display stopped working. So I decided to re-install the