My Brain in 3D: Rendered Videos and Images of My fMRI Scan Data

My brain (c 2007).
My brain (c 2007).

Back in 2007, I made a deal with a friend to participate in his fMRI brain scan study at the University of Liverpool in exchange for a copy of the DICOM data from my scan. He agreed to the trade.

Since then, I occasionally pull my scan data off the shelf and dust off the cobwebs and disk errors, and import it into the DICOM Viewer, OsiriX (e.g., as I did in 2009). With the latest versions, I have had a lot of trouble importing the files as they were given to me into OsiriX. Luckily, I saved the installers for earlier versions including the venerable version 3.5.1, which still runs fine on MacOS X Mavericks and Yosemite.

Using OsiriX’s many features, I created these four videos and an album of images of my 2007 brain. I wonder how it has changed since that time–completing my MA, then PhD, taking a postdoc at Georgia Tech, and now, working at City Tech. Also, I think about the technologies of representation that make it possible for me to see my brain without injury or invasion–OsiriX and unseen software libraries for working with, manipulating, and displaying DICOM data, MacOS X and its technology APIs, my MacBook Pro retina, disk and flash drives, email (how I originally received the scan data), the fMRI machine that I sat in for 30 minutes to an hour, the physical laws behind each technology and the biology of myself, etc. What do you think about when you see my brain represented below?

Final Videos

Draft Video (I had not yet removed all the tissues and bone around the brain)

Rendered Images

https://www.flickr.com/photos/dynamicsubspace/sets/72157647825318882/

Lego Building Experiments with Google Glass, Thoughts on Its Potential for Interdisciplinary Humanities Research

Since I received my Google Glass last week, I have been learning how to wear and use it. Ultimately, I want to incorporate Glass into my Retrocomputing Lab research workflow. I am interested in the experience of using computer hardware and software (something that I have been interested in for a long time and wrote about as an undergraduate), so Glass will provide a way of capturing some of my phenomenal experience–perspective, vision, and sound. I can provide oral commentary of my haptic and olfactic experiences (yes, computers have unique smells–something that helps store/recall memories and emotions) while also recording thoughts, memories, and asides that enrich my shared video experience. As one component of the digital humanities, I want to create an archive of my raw research of working with computers and their software that others can use, draw inspiration from, or comment on through their own research, writing, and teaching.

For the work that I do in my personal Retrocomputing Lab, I will use Glass as one more tool among a variety of other technologies that enable my research. Glass will add another data layer–itself richly textured and layered with audio/video/Internet/software capabilities–to the research that I do. Due to the ease of sharing images and video in real time, I can immediately make my in-process research available on YouTube, Twitter, and here on dynamicsubspace.net. Furthermore, my research will be useable by others–hobbyists, students, and other researchers in many interdisciplinary fields. Glass will join my non-real time distribution of data on paper, computer written notes (though, I could make these freely viewable in realtime on say, Google Drive), and published research.

Finally, I am interested in the mixing of old and new technologies. Glass meets its ancestors in the IBM PC and Macintosh. Glassware meets DOS, Windows 3.1, and System 7. I want to explore how the intermingling of these technologies leads to new insights, connections, and elaborations. While I am only speculating, I strongly believe that Glass and similar wearable computing technologies will elevate the outcomes and knowledge produced in humanities research–conceptualized as interdisciplinary like mine or not.

The videos included in this post were tests of the manually extended video recording feature. They don’t involve the Retrocomputing Lab, because how I want to use Glass to record my work will involve more and different kinds of planning. I used what I had at hand to test out Glass’ video capabilities included below.

Glass Video from Apr 22, 2014, Lego Build of The Batman Tumbler 30300 Polybag

Glass Video from Apr 24, 2014, Target Exclusive Lego 30215 Legolas Greenleaf Polybag

Followup to Adventures with a CustoMac: Installing Mac OS X Mavericks on Asus P8Z77-V PC

Mavericks installed on CustoMac. NB: MBPr on desk and PowerMacintosh 8500/120 on right.
Mavericks installed on CustoMac. NB: MBPr on desk and PowerMacintosh 8500/120 on right.

Last summer, I wrote about my experiences installing Mac OS X 10.8 Mountain Lion on my Asus P8Z77-V and Intel i7-2700K PC here. What I neglected to say at the time was that an alarming number of creeping instabilities led me to ultimately abandon running Mountain Lion on my PC and return to Windows 7.

I later learned that some of these instabilities were likely linked to a bad PSU and video card–both of which were replaced by the manufacturers under warranty (awesome kudos to Antec and EVGA). With the new PSU and video card, my PC returned to 100% stability under Windows 7. This made me wonder if I could try rolling out a Mavericks installation on my PC.

Also, I wanted to use Mac OS X’s superior file content search technology and other third-party textual analysis tools in my research. I have a MacBook Pro 15″ retina (MBPr), but it lacks the hard drive capacity for my accumulated research files. The comfort that I feel in the MacOS environment and the need for lots of fast storage led me to turn my attention back to turning my PC into a CustoMac (aka “hackintosh”).

This time, I wanted to streamline and simply my setup as much as possible and incorporate components that should work out of the box (OOB). Toward this end, I reduced my hardware configuration from this:

  • ASUS P8Z77-V LGA 1155 Z77 ATX Intel Motherboard (disabled on-board Intel HD 3000 video and Asus Wi-Fi Go! add-on card)
  • Intel Core i7 2700K LGA 1155 Boxed Processor
  • Corsair XMS3 Series 16GB DDR3-1333MHz (PC3-10666) CL 9 Dual Channel Desktop Memory Kit (Four 4GB Memory Modules)
  • evga 01G-P3-1561-KR GeForce GTX 560 Ti 1024MB GDDR5 PCIe 2.0 x16 Video Card
  • Antec High Current Gamer 750W Gamer Power Supply HCG-750
  • Corsair Vengeance C70 Gaming Mid Tower Case Military Green
  • Cooler Master Hyper 212 Plus Universal CPU Cooler
  • Samsung 22X DVD±RW Burner with Dual Layer Support – OEM
  • Intel 128 GB SATA SSD
  • Western Digital Caviar Green WD10EARX 1TB IntelliPower 64MB Cache SATA 6.0Gb/s 3.5″ Internal Hard Drive – Bare Drive
Using on-board video and no ASUS wifi card.
Using on-board video and no ASUS wifi card.

to this:

  • ASUS P8Z77-V LGA 1155 Z77 ATX Intel Motherboard (using on-board Intel HD 3000 video and removing Asus Wi-Fi Go! add-on card)
  • Intel Core i7 2700K LGA 1155 Boxed Processor
  • Corsair XMS3 Series 16GB DDR3-1333MHz (PC3-10666) CL 9 Dual Channel Desktop Memory Kit (Four 4GB Memory Modules)
  • evga 01G-P3-1561-KR GeForce GTX 560 Ti 1024MB GDDR5 PCIe 2.0 x16 Video Card (removed to simply setup and save power–who has time for gaming?)
  • Antec High Current Gamer 750W Gamer Power Supply HCG-750
  • Corsair Vengeance C70 Gaming Mid Tower Case Military Green
  • Cooler Master Hyper 212 Plus Universal CPU Cooler
  • Samsung 22X DVD±RW Burner with Dual Layer Support – OEM
  • Intel 128 GB SATA SSD
  • Three Western Digital HDDs for file storage and work space. 
IoGear GBU521 and TP-Link TL-WDN4800 from Microcenter.
IoGear GBU521 and TP-Link TL-WDN4800 from Microcenter.

Also, I added two new components that were recommended from the TonyMacx86 Forums:

  • TP-Link 450Mbpx Wireless N Dual Band PCI Express Adapter (TL-WDN4800). It works in Mavericks OOB.
  • IoGear Bluetooth 4.0 USB Micro Adapter (GBU521). It works in Mavericks OOB.
DSC01487
ASUS’s Wi-Fi Go! card works great in Windows 7, but it caused problems with my Mavericks installation.

As noted above, I physically removed my 560 Ti video card, because I wanted to simply my setup for installation purposes. Also, I removed the ASUS Wi-Fi Go! add-on card, because despite disabling it in BIOS, the Mavericks installer seemed to hang on a wi-fi device while attempting to set its locale (a setting that determines what radio settings to use based on the country that you happen to be in). After I removed the Wi-Fi Go! card, I had a nearly flawless Mavericks installation process (NB: removing the Wi-Fi Go! card required removing the motherboard, turning it over, removing a screw holding in the Wi-Fi Go! card, turning the motherboard over, and unplugging the Wi-Fi Go! card).

These are the steps that I used to install Mavericks on my PC:

  1. Follow TonyMac’s Mavericks installation guide for making an installation USB drive and installing Mavericks.
  2. Following installation of Mavericks, boot from your USB drive, select your new Mavericks installation drive, arrive at the desktop, and run Multibeast.
  3. Select these settings in Multibeast:
    1. Quick Start > DSDT Free (I left all pre-selected options as-is. Below are additional selections that I made.)
    2. Drivers > Audio > Realtek > Without DSDT > ALC892
    3. Drivers > Disk > 3rd Party SATA
    4. Drivers > Graphics > Intel Graphics Patch for Mixed Configurations
    5. Drivers > Misc > Fake SMC
    6. Drivers > Misc > Fake SMC Plugins
    7. Drivers > Misc > Fake SMC HWMonitor App
    8. Drivers > Misc > NullCPUPowerManagement (I don’t want my machine to go to sleep)
    9. Drivers > Misc > USB 3.0 – Universal
    10. Drivers > Network > Intel – hank’s AppleIntelE1000e
    11. Customize > 1080p Display Mode
    12. Build > Install
  4. Repair Permissions on Mavericks drive from /Applications/Utilities/Disk Utility
  5. Reboot
  6. Run Chameleon Wizard (this will fix a problem that you might have with connecting to the App Store)
  7. Click SMBios > Edit > Premade SMBioses > choose MacPro 3,1 > Save
  8. Reboot
  9. CustoMac should now be fully operational!

In order to arrive at the above instructions, I read a lot of first hand experiences and third party suggestions on TonyMac’s forums. I owe a tremendous debt of gratitude to the amazing community of CustoMac builders who take the time to share their thoughts and lessons and equally so to the tool-builders who create amazing software including UniBeast, Multibeast, and Chameleon Wizard!

I would suggest that you remember that there is not always one path to a successful build. I distilled a lot of posts into my successful build. Your experience with similar hardware might take a different path. Reading others experiences and trying their suggestions experimentally can lead to your own successful discoveries. Thus, I took the time to try out different configurations of hardware until settling on the stripped down approach with on-board video and OOB networking gear. I tried several different installations: a failed Mavericks installation with kernel panics (Wi-Fi Go! card installed and wrong Multibeast configuration), a successful Mountain Lion installation (barebones and correct Multibeast configuration), and a successful Mavericks installation (detailed above).

Obviously, MacOS X can run on a wide range of PC hardware given the correct drivers, configuration information, etc. Apple could do great things if only Tim Cook and others would think differently and move beyond the tightly integrated hardware-software experience. Apple’s engineers could do great things with building better operating systems that adapt to a person’s hardware. Given the chance, they could challenge Microsoft and Google with a new MacOS X that is insanely great for everyone–not just those who can afford to buy new hardware.

Now, back to using some of the tools that I use in my research on a computing platform that I enjoy:

Review of Donald E. Hall’s The Academic Self: An Owner’s Manual, Recommended for Graduate Students, Postdocs, and Junior Faculty

Hall, Donald E. The Academic Self: An Owner’s Manual. Columbus: Ohio State UP, 2002. Print.

I picked up Donald E. Hall’s The Academic Self from the Georgia Tech Library after completing my teaching assignment for Spring 2013–eleven years after the book had been published. Specifically, I was looking for books and articles to help me grapple with the challenges of this stage of my professional life as a postdoctoral fellow: teaching a 3-3 load, performing service duties, researching, writing,  receiving rejections (and the far less often acceptance), and applying for permanent positions. In the following, I summarize Hall’s arguments, provide some commentary, and close with a contextualized recommendation.

Hall states in the introduction that the goal of The Academic Self is, “encourage its readership to engage critically their professional self-identities, processes, values, and definitions of success” (Hall xv). I found this book to be particularly useful for thinking through my professional self-identity. As I was taught by Brian Huot at Kent State University to be a reflective practitioner in my teaching and pedagogy, Hall argues for something akin to this in terms of Anthony Giddens’ “the reflexive construction of self-identity” (qtd. in Hall 3). Hall truncates this to be “self-reflexivity,” or the recognition that who we are is an unfolding and emergent project. I use this blog as part of my processes of self-reflection–thinking through my research and teaching while striving to improve both through conscious planning and effort.

However, unlike the past where the self was static and enforced by external forces, modernity (and postmodernity–a term Hall, like Giddens, disagrees with) has ushered in an era where the self is constructed by the individual reflectively. From his viewpoint, the self is a text that changes and can be changed by the individual with a greater deal of agency than perhaps possible in the past (he acknowledges his privileged position earlier in the book, but it bears repeating that this level of agency certainly is not equally distributed).

In the first chapter, titled “Self,” Hall writes, “Living in the late-modern age, in a social milieu already thoroughly pervaded by forms of self-reflexivity, and trained as critical readers, we academics in particular have the capacity and the professional skills to live with a critical (self-) consciousness, to reflect critically upon self-reflexivity, and to use always our professional talents to integrate our theories and our practices” (Hall 5). If we consider ourselves, the profession, and our institutions as texts to be read, we can apply our training to better understanding these texts and devise ways of making positive change to these texts.

He identifies what he sees as two extremes that “continue to plague academic existence: that of Casaubonic paralysis and Carlylean workaholism” (Hall 8). In the former, academics can be caught in a ignorant paranoia like Casaubon of George Eliot’s Middlemarch (1871-1872), or in the latter, academics can follow Thomas Carlyle’s call to work and avoid the “symptom” of “self-contemplation” (qtd. in Hall 6).

In the chapter titled “Profession,” Hall calls for us to apply our training to reflective analysis and problem solving of our professional selves and our relationship to the ever changing state of the profession itself. He questions to what extent the work of professionalism (seminars, workshops, etc.) are descriptive or prescriptive. “The ideal of intellectual work” varies from person to person, but it is an important choice that we each must make in defining who we are within the profession.

He reminds us that, “much of the pleasure of planning, processing, and time management lies not in their end products–publication or project completion–it is derived from the nourishment –intellectual, communal, and professional–provided by the processes themselves” (Hall 46). He builds his approach to process on his personal experiences: “Unlike some, I know well when my work day is over. Part of the textuality of process is its beginning, middle, and most importantly, its end” (Hall 46).

His talking points on process are perhaps the most practical advice that he provides in the book. In planning, he advises:

  1. begin from the unmovable to the tentative in your scheduling, know yourself–plan according to your habits and work on those aspects of your planning that need adjustment, and stick to your well planned schedule to yield the personal time that you might be lacking now without such a plan
  2. break goals and deliverables into their constituent parts [or building blocks (my Lego analogy) or code (my programming analogy)]
  3. monitor your progress and see daily/smaller goals as ends in themselves rather than simply means to a greater end
  4. take ownership of your goals, schedule, and commitments to others [this is something that I carry forward from my Mindspring days: Core Values and Beliefs: Do not drop the ball.]
  5. deal with and learn from setbacks–life, bad reviews, rejections, etc. [this is easier said than done, and the external effects of bad reviews goes beyond its effect on the writer]
  6. let change happen to our goals and research as our workplace, interests, and circumstances change
  7. taking ownership of our work in these ways can help protect us from and strengthen us against burnout

Hall goes on to suggest ten steps for professional invigoration to help folks suffering from a stalled career or burnout. However, these ten pieces of advice are equally applicable to graduate students, postdocs, and beginning faculty: join your field’s national organization, read widely in your field, set precise goals, maintain a daily writing schedule [my most difficult challenge], present conference papers, write shorter artifacts to support your research [reviews or my case, this blog], know the process and timeline of manuscript publishing, foster relationships with publishers and editors, politely disengage from poor or dysfunctional professional relationship/praise and value positive relationships, and find support in your local networks.

The final chapter, “Collegiality, Community, and Change,” reminds us, “always t put and keep our own house in order” (Hall 70). He suggests strategies counter to what he calls “the destructive ethos of ‘free agency’ that seems to pervade the academy today–the mindset that institutional affiliations are always only temporary and that individuals owe little to their departments or institutions beyond the very short term” (Hall 70). On professional attitudes, he encourages a focus on the local (institution) before national (beyond the institution), the current job as potentially your last job–treat it with that respect, meet institutional expectations, collegial respect of others, and learning the history of our institution/school/department from everyone with whom we work.

Perhaps most notably, he writes, “If we measure our success through the articulation and meeting of our own goals, as I suggest throughout this book, we can achieve them without begrudging others their own successes. However, if we need to succeed primarily in comparison to others, then we are deciding to enter a dynamic of competition that has numerous pernicious consequences, personal and inter-personal” (Hall 74-75). As I have written about on Dynamic Subspace before, it was the overwhelming in-your-faceness of others’ successes on social media like Facebook that distracted me from my own work. Seeing so many diverse projects, publications, and other accomplishments made me question my own works-in-progress before they had time to properly incubate and grow. For all of social media’s useful and positive aspects for maintaining and growing networks of interpersonal relationships, I had the most trouble resisting the self-doubt that the Facebook News Feed generated for me.

Finally, he encourages dynamic and invested change in departments and institutions. However, as junior faculty, it is important to research and weigh the possible repercussions for working to make change. Hall is not arguing against change by those without tenure, but he is warning us to proceed cautiously and knowledgeably due to a number factors: potential sources of resistance, jeopardizing our jobs, etc.

Hall’s “Postscript” reinforces the overarching idea of ownership by calling on the reader to live with “intensity,” an idea that inspired Hall from Walter Pater’s 1868 The Renaissance: “burn always with [a] hard, gem-like flame” (qtd. in Hall 89). Hall’s intensity is one self-motivated, well-planned, dynamically agile, and passionately executed.

Hall’s The Academic Self is a very short read that is well worth the brief time that it will take to read. It offers some solid advice woven with the same theoretically infused self-reflexivity that he encourages. It practices what it preaches. The main thing to remember is that the book is eleven years old. When it was published, the field of English studies was experiencing an employment downturn (albeit one not as pronounced as in recent years). Michael Berube’s “Presidential Address 2013–How We Got Here” (PMLA 128.3 May 2013: 530-541), among many other places–this issue just arrived in the mail today, so I was reading it between chapters of Hall’s book, picks up some of the other challenges that graduate students, postdoctoral fellows, and junior faculty have to contend with in the larger spheres of the profession and society. The other advice that Hall provides on personal ownership and collegiality, I believe, remains useful and inspirational. In addition to reading Hall’s book, you should check out his bibliography for further important reading in this vein.

Play | Retrocomputing, Platform Studies, and Digital Archiving Session, THATCamp SE 2012 at Georgia Tech, Sunday at 9:30am

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This morning, Becky, Robyn, Aaron, Chris, and Colin joined me for the Play | Retrocomputing 9:30am session at THATCamp SE 2013 at Georgia Tech. Aaron recorded our lively and interesting conversation on the shared GoogleDoc available here (along with notes from all of the sessions).

Above, you can see pictures that I took while we were playing, working, and talking. Our conversation veered from materiality of experiencing old software on original computing hardware to archiving/preserving old computer and software artifacts.

The computers that I brought to kickstart our conversation were a Powerbook 145 and Powerbook 180c.

Other conversations from THATCamp SE 2013 are on Twitter with the #thatcampse13 hashtag.