emissions from the polluted tube

neuroimaging & python

stnava — Sat, 05 Nov 2011 20:18:05 +0000

download the 32bit epd python install from

www.enthought.com/products/epd.php

then at command line

easy_install nibabel

then in a new shell do:

ipython notebook –pylab=inline

and start a new notebook

then try typing a latex equation by switching to doc mode ( type ctl m m ) and then type (verbatim) $t=\int_0^1 dt$

then try :

from time import localtime
# record how long this takes
print localtime()
import numpy as np
import scipy.ndimage as ndimage
import nibabel as nib
import matplotlib as mpl
from scipy import *
ion()

path_to_images=’/Users/stnava/code/ipython/’
img1 = nib.load(path_to_images+’img1.nii.gz’)

imshow(smooth_image[:,:]>220)

octopush

stnava — Sat, 30 Jan 2010 15:25:50 +0000

the eight legs of my mind are each grabbing something different::

a gmm-mrf with spatial priors deforming and finding the best possible local world to settle into of all those in the universe.

a longitudinal analysis, accurate, multivariate and counting the millimeter changes that undermine your thoughts.

a world where we can picture, enumerate and correct the biases in the things we do.

a comparison of brain extractions by a stodgy old man.

the hippocampus grows under nurturance in females and shrinks in males …. who can explain this?

images of babies and counting their growth, failure to thrive, the fat the superfood jet fuel builds.

a contribution to the arxiv?

my first act of free will is to believe in free will

stnava — Tue, 22 Dec 2009 05:54:46 +0000

william james wrote that.

s.l.o. slowbispo. rain.

stony gray faces looking skyward.

pregnant women produce shizophrenic babies.

or diplomatic, presidential babies?

maybe the curve is u-shaped and the lines we imagine dont fit.

the answer is looking for the answer … and looking again.

plod the data. heave it on your shoulder. swim in it.

putting one foot after the other gets you somewhere.

from the city

stnava — Sat, 14 Nov 2009 21:07:15 +0000

working, writing, a cloudy day with a passing offshore low + hurricane ida remains — i am watching the cameras along the coast and the many waves in their many forms bending into the coves, open beaches and jetties along our J-shaped coast. the more one surfs, the more one will surf. and today my account drained some small percentage off my future. maybe this work will serve to free me in old age, when i will be happy just to paddle out and stand up a few times, and i often wonder why i am not a carpenter in the outer banks, an engineer on the space coast or just living in san diego as an asshole, but an asshole who surfs blacks every other day. instead i am less an asshole, maybe, surviving in the sea-less city.

sunny with a black moon

stnava — Mon, 09 Nov 2009 21:19:56 +0000

a cracked japanese tea cup, scars along her arms from scalding bath water and straight razor attention, a thin set of full curves drawn by a ghostly genetic painter and dressed in green with a smile and sad eyes, a flat, grassy plane next to a cold, flowery mountain, an old brown surfboard with knees and elbows and foreheads impressed and glassed-over cracks, these imperfect things that i love!

bricks

stnava — Sun, 08 Nov 2009 13:31:02 +0000

you have things to do without end, one is stacked upon another, you work like a bricklayer and as the mortar appears to set, the brick bursts and the same job is back like a bill collector … that’s about how i feel right now. here is the list of these slippery things which will be much shorter than it feels :

revise cca paper, ASAP

renewal app for LRP — ASAP, Agh!

lead murray’s studies : cca on subtypes + longitudinal studies on whatever we have , dec. 1. == currently working on statistical design

finalize oasis study processing — determine parameter effect on power, Working On.

ANTS paper — multivariate analysis results + time parameterized SyN results for labeling, ASAP == need to revise

slides for jim’s trip to beijing, unknown due date.

SPR abstract due the 18th

work on Hoon’s evaluation study

recommendation for pluta — this month

ISMRM abstracts due the 10th == X’d Nov. 10

connectome project writing — should do today! == X’d Nov 9.

draft letter for job requirements : columbia u & upenn & ucla? == X’d Nov. 10

and, finally, fix ANTS to work on gcc4.3 with ubuntu (probably resolved already) == X’d Nov 9.

plan lab meeting for Thursday == X’d Nov 9.

also, the surf will be potentially great thursday to sunday as it should be in november in new jersey.

dark surf

stnava — Fri, 06 Nov 2009 21:25:12 +0000

some of the most memorable days were those that would be near impossible to capture on film ...

ants exceptions

stnava — Fri, 06 Nov 2009 21:06:03 +0000

a mystery problem with ants — at mit, segmentation faults are being thrown in the tests and without any explanation … stay tuned for the solution, if there is one.

a few hours later >> after polling people in the lab, i believe we isolated the problem. there is a function that uses a b-spline approximation to a curve in order to help us determine convergence — it is invoked at exactly the time at which the exception occurs …. we do not know the specific solution yet, but have an educated guess at one.

this is now fixed — Nov. 9 th verfication. And, interestingly, just in time to head off a number of users’ asking about this problem! thanks, Satra!

spot A ese swell

stnava — Fri, 06 Nov 2009 21:04:21 +0000

that special spot we love showed three faces today :

1 clean and inconsistent chest high semi-barrels peeling at high tide …. by the time we paddled out, the waves were passing by on the outside bar, avoiding our chosen jetty. and the one regular girl i’ve seen surf spot A for years showed up to make the person-to-wave frequency ratio about three to one every fifteen minutes. not happy after seeing a few beauties roll through this same spot fifteen minutes earlier with no soul out.

2 light onshore breaking in the chest+ range at mid-low tide and mid-beach peak. very fun when they came through – fast runners begging to be chased up and down the face. some satisfying hacks.

3 low tide and the wind picked up — dredgers coming out of the flatness and breaking waist high in about a foot of water. stand and wait on the sandbar as the current rushes around you. step off the ledge into the deep, turn, paddle, stand up, pull into a sand bottom tube … we moved down the beach and caught 150 yard waist high waves with chop all over them —– named that bumpy wave, on that day, “the rickety railroad.”

today’s questions about the brain

stnava — Fri, 06 Nov 2009 20:56:06 +0000

met about imaging babies today — how do their brains change as they learn to crawl, walk, speak, smile? why do some children fall behind others, developmentally, by twelve months of age?

similar questions in the elderly brain — what is happening as memory, speech or fluid motion decay away?

are these differences in connectivity or in computational structures of the brain?