Wandell Lab Meetings

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The Wandell lab meets Monday mornings at 11am in room 419, Jordan Hall.

The Vision Lunch meetings are on Wednesdays at 11:30.

Contents

[edit] 2014

[edit] January

13 - Hiromasa Takemura Practice Talk for Osaka

"20 - Haoxing on PoST and Computations"

[edit] February

RESCHEDULED - Journal Club: Traumatic Brain Imaging:

http://www.ajnr.org/content/29/5/967

http://onlinelibrary.wiley.com/doi/10.1002/ana.23783/full

http://www.nejm.org/doi/full/10.1056/NEJMp058102

http://www.ajronline.org/doi/abs/10.2214/ajr.150.3.663

http://www.sciencedirect.com/science/article/pii/S221315821300168X

10 - Palanker / Chichilnisky

[edit] March

3 - Talk Kai Miller

[edit] April

21 - Kristen Yeom

[edit] Oct

20th James Rioux

[edit] 2013

[edit] January

Jan 7. Kendrick practice

Jan 14. Trevor Hastie group (Ariel)

Jan. 21 Jon Winawer and Hiroshi

Jan. 28 Aviv and Jason

[edit] February

Feb 11 Franco Practice Job Talk

Feb. Hiromasa hV4 and VOF

[edit] March

[edit] April

15th

22nd - ISMRM

29th - Dora/Jon/Gamma


[edit] May

6th - ISMRM Rehash

13th - VSS (people away)

20th - Jason arranges with Anne Fernald's group

27th - Minnesota (Jon, Kendrick, and Brian)

[edit] June

3rd - Adrian update on vistasoft

10th - Shumpei on LHON/JMD

17th - HBM

24th - Mark Schira

[edit] July

1st

8th - Rainer Goebel

15th - Tahoe meeting

[edit] 2012


[edit] APRIL

[edit] April 2

Franco

[edit] April 9

Ariel

[edit] April 16

Yuon Deng

[edit] April 23

Christine Nordahl, David Amaral, Ryan Johnson

[edit] April 30

Wandell away (NAS)


[edit] MAY

  • VSS 2012 will be held at the Waldorf Astoria Naples May 11-16, 2012

[edit] May 7

Arvo Meeting (Wandell away)

[edit] May 14

Jessica Thesis Defense

[edit] May 21

Winawer

[edit] May 28

Kendrick


[edit] JUNE

[edit] June 4

Wandell away

[edit] June 11

Joint with Newsome lab: Valerio and Roozbeh

[edit] June 18

Jason Yeatman

[edit] June 25

Wandell away (SB)


[edit] JULY

[edit] July 2

Wandell away

[edit] July 9

Dora Hermes (ECoG & fMRI)

[edit] July 16

Hiromasa (Planning for diffusion measures and the future)
Perhaps a little Kendrick.

[edit] July 23


A brief show from Nathan.

[edit] July 30


[edit] AUGUST

[edit] August 3 (FRIDAY, rm 417)


Ana Radonjic (UPenn, postdoc)
An informal talk on eye movements and color appearance

[edit] August 6

Bijan Pesaran, NYU Faculty. Coherent patterns of neural activity supporting coordination and decision.

[edit] August 13

David Susillo, following up the material from Valerio.

[edit] August 20


[edit] August 27


Brian Away.

[edit] SEPTEMBER

[edit] Sept. 3


[edit] Sept. 10


[edit] Sept. 17


[edit] Sept. 24


[edit] OCTOBER

  • Neuroscience 2012, SfN's 42nd annual meeting, is scheduled for Oct. 13 -17 in New Orleans at the Ernest N. Morial Convention Center.


[edit] NOVEMBER


[edit] DECEMBER

<5> Franco Practice talk.

10 Franco Practice talk.

[edit] 2011

[edit] January

Jan. 10th - Brian and Jon discuss grant specific aims

Jan. 17th - Aviv practices for Israel

Jan. 24th - Jessica ? Hiroshi?

Jan. 31

Professor Tsuchiya (hosted by Parvizi)

A fundamental question in cognitive neuroscience is how neuronal representations are related to conscious experience. Two key questions are: where in the brain such representations are located, and at what point in time they correlate with conscious experience. In line with this issue, a hotly debated question is whether primary visual cortex (V1) contributes to visual consciousness, or whether this depends only on higher order cortices. Here we investigated this issue by recording directly from early visual cortex in two neurosurgical patients undergoing epilepsy monitoring with intracranial electrocorticogram (ECoG) electrodes that covered early visual cortices, including the dorsal and ventral banks of the calcarine sulcus. We used Continuous Flash Suppression (CFS) to investigate the time course of when ‘invisible’ stimuli broke interocular suppression. Participants were asked to watch faces presented under CFS, to push a button when they started to see any part of the face, and then to indicate its spatial location. This occured over several seconds. During the task performance we recorded intracranial ECoG at high spatiotemporal resolution from all contacts in parallel. We used multivariate decoding techniques and found that the location of the invisible face stimulus became decodable from neuronal activity ~1.8 sec before the subject’s button press. Counter-intuitively, the same cortical sites from which we were able to decode this predictive signal showed a decrease in activity immediately prior to the transition from invisibility to visibility. Furthermore, we observed an increase in coherence among widely separated electrodes during the invisible epoch, which collapsed to a focal ensemble when the stimulus became visible. These results suggest that diffuse coherent representation is insufficient for visual awareness and that locally specialized patterns of activation may be key to consciousness. Our findings are consistent with one recently proposed framework for understanding consciousness utilizing information integration theory (Tononi, 2008).

[edit] February

Feb. 7th

Feb. 14th

Feb. 21st

Feb. 28th

[edit] March

March 7th

March 14th

March 21st

March 28th

[edit] April

[edit] April 4

1. Let’s discuss summer interns and research plans at tomorrow’s meeting.

  • One intern from Davis, one from SMS, one Sherbondy recommendation. One may go to the CNI, the others have nothing nailed down, but Franco and Jason may take the two others.

2. We can make a plan for some readings in the coming weeks – I know that Jon had something he wanted to go over pertaining to high field. Perhaps there are other articles or topics that some of you would like us to review together.

  • Lab members should make suggestions.

3. Discuss whether we should submit a renewal for the 2nd RO1 in early July, and if so what will be required. We can discuss the overall grant support situation at that time.

  • Might focus on meodeling BOLD signals. Need to look at preliminary data and decide. (32nd year of renewals). Start with Kendrick? This is the time, this is the future, this is it!

4. I would like to develop some specificity on lab software needs.

  • QUENCH: We don't have access to parts of the code that we want to have. Trival changes are not possible. We need someone who will be able to learn the code and be able to make changes. <BOB> The code is modular, as is the matlab code. <BRIAN> Not worried about the matlab stuff. ISSUES: Being able to load ROIs as binary images and make changes - that are saved. Jason is passionate about helping with this.
  • UBUNTU vs FEDORA: Push Martin toward Ubuntu. Neurodebian is the main reason to move to Ubuntu. <BRIAN and MICHAEL> Lean on Martin to switch the computers over to Ubuntu.

5. Clarity on the set of papers and projects that are cued up and getting ready for submission, or in a somewhat earlier stage of preparation.

6. CNI - Bob

  • DTI: Stock GE sequence for DTI seems to be working well. Reverse polarity DTI scans coming soon. Will have a working field-based correction soon. Franco wants to put his head in the scanner.
  • Anonymyze data: Security of the data PI responsibility. Scanner is on a closed network, secured behind a firewall. <BOB> Has the source code for the EPI sequence, but not the recon.

7. CNI Technology Meeting:

  • Jon will organize the paper, a time to be set later.

8. Jon: On KNK code

  • Has written some code that integrates KNK code with Vistasoft, will add it to vistaproj.

[edit] April 11: Danial Lashkari from MIT

Search for Functional Specificity in the Brain: A Basic Exploratory Framework for Group fMRI Analysis

Functional MRI studies have uncovered a number of brain areas that demonstrate highly specific functional patterns. In visual object recognition, for instance, regions selective for faces, places, and bodies have been robustly identified along the ventral visual pathway. In the search for functionally specific areas, fMRI investigators in vision and other domain commonly use confirmatory analyses. They first hypothesize a candidate pattern of functional specificity and then design and perform an experiment that enables the detection of brain areas that show the pattern of interest. The validation of such hypotheses usually involves an assessment of the spatial consistency of the detected areas across subjects. In this work, we develop an alternative exploratory setting for the design and analysis of fMRI studies that overcomes some of the basic limitations of the traditional confirmatory approach. First, we automatically search all likely patterns of functional specificity, instead of manually testing hypotheses one-by-one. Second, we relax the spatial consistency constraint to enable the discovery of likely networks that do not appear in or around the same location in brains of different subjects. We apply the method to a study of high level vision where we consider a large space of patterns of category selectivity over 69 distinct images. Although the method is not informed about the category structure among stimuli, it successfully discovers face, scene, and body selective areas, among a few others, as the most prominent patterns in the data. This finding suggests that our approach can be employed to search for novel patterns of functional specificity in high level perception and cognition.

[edit] April 18

Directory structure edits DTI ANATOMY

These top-level directories will have soft-links to all of the data that we have spread out over all the data directories. Michael will make the call regarding naming structure and location. Soft-links can be created as part of the dti and anatomy processing streams.

Each subject's directory will have an info.mat file that will have important information regarding that subject's scan (e.g., b-value, age, directions, resolution etc.). This will provide a way to "search" for data that meet a certian criteria.

Franco has some ideas about DTI folder organization and multiple aquisitions.

[edit] April 25

H&R

[edit] May

[edit] May 2

Brian away - No lab meeting.

[edit] May 9

VSS meeting in FLA - no lab meeting.

[edit] May 16

[edit] May 23

[edit] May 30

[edit] June

[edit] June 6

[edit] June 13

[edit] June 20

[edit] June 27

[edit] July

[edit] July 4

[edit] July 11

[edit] July 18

[edit] July 25

Jessica: TBSS

[edit] August

[edit] August 1

Demian Wassermann, PhD demian@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA

Automated In Vivo Dissection of White Matter Structures from Diffusion Magnetic Resonance Imaging and Their Subsequent Statistical Analysis

The motivation of this talk is the in vivo dissection of the human brain's white matter from diffusion magnetic resonance imaging. This procedure isolates the human brain's white matter tracts that play a role in a particular function or disorder of the brain so they can be analyzed. Manually performing this task requires a great knowledge of brain anatomy and several hours of work. Hence, the development of a technique to automatically perform the identification of white matter structures is of utmost importance. The brain is organized in networks that are made up of tracts connecting different regions. These networks are important for the development of brain functions such as language or vision. Moreover, lesions and cognitive disorders are sometimes better explained by disconnection mechanisms between cerebral regions than by damage of those regions. Despite several decades of tracing these networks in the brain, our knowledge of cerebral connections has progressed very little since the beginning of the last century. Recently, we have seen a spectacular development of magnetic resonance imaging (MRI) techniques for the study of the living human brain. One technique for exploring white matter tissue characteristics and pathways in vivo is Diffusion MRI (dMRI). Particularly, dMRI-based tractography facilitates tracing the white matter tracts in vivo. Overall, dMRI is a promising technique to explore the anatomical basis of human cognition and its disorders. In this talk, I develop the means for the automatic dissection of WM tracts from dMRI, this is based on a mathematical framework for the WM and its tracts based on the Gaussian process formalism. Using this framework, we develop techniques to dissect the white matter, register fiber bundles and find group differences in the white matter, particularly between healthy and schizophrenic subjects.

Bio: Demian graduated from the University of Buenos Aires, Argentina, where he obtained his B.Sc in computer science. He obtained his PhD at the Athena (formerly Odyssee) research team at the INRIA Sophia Antipolis-Mediterranee under the supervision of Professor Rachid Deriche. In his PhD he focused on the analysis of white matter fibers traced from Diffusion MRI, aiming at providing a sound mathematical framework for automatic dissection and statistical analysis of the structures of the human brain's white matter. Since May 2010, Demian is working under the joint supervision of Professor Shenton at the PNL, Professor Westin at the LMI and Professor Kikinis at the SPL, all three laboratories at the Harvard Medical School and the Brigham and Women's Hospital.

[edit] August 8

[edit] August 15

[edit] August 22

Ryan and Stephanie to present their summer research.

[edit] August 29

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