Kurage [水母] is Japanese for jellyfish and is pronounced ku-ra-geh
Welcome
Welcome to the NIMH MEG Core Facility website. Here you can find information ranging from local operations of the lab, to general topics on the analysis of MEG data, including software available for download.
Clicking on the recent changes link here or at the bottom of every page gives you a list of all the recently modified pages. It's an easy way to see what's new on the site. The recent changes are also available as an RSS feed.
Also, the Search box (at the bottom of the sidebar to the left) is a powerful way to find things on this website.
See our NIMH IRP Retreat poster, available in PNG and PPT formats (~1.6 MB).
Latest News
A 3dcalc command has been added to the MEG Analysis pages for converting SAM pseudo-F ratios to log ratios. See
here.
Happy Turkey Day, or Duck Day, or Ham Day, or Eggplant Lasagna Day, as the case may be. By the way, /data6 on Tako is full and most people are pushing data to /data7 now by default. ~/data symbolic links have been adjusted to reflect this and ~/data6 links have been made available.
Richard Coppola, director of the NIMH MEG Core Facility, displayed astonishing electromechanical talent by successfully repairing the power supply. The system is up and running. Click
here for pictures.
It turns out that the reason the new power supplies failed is that one of the cables connecting the supply to the rack is an old version that is no longer used. Now that we know this, we are getting one of the new supplies (which had been shipped back), and we will reconfigure the cable. We should have all of this done Monday morning. We're sorry for the inconvenience.
The 3.3 volt power supply in our MEG rack started to fail. We replaced the entire power supply, which includes a 5 volt supply. Guess what? The new 5 volt supply was DOA. So we switched back to the old power supply, which, though it is failing, is at least doing so intermittently. The new 5 volt supply is completely dead.
Hey, it's time for the NIMH Retreat again! Check out our poster (link at the right). See you in scenic Gettysburg, PA!
The warmup and cooldown was successful, and we are resuming normal operations on Tuesday.
Last week before we get our vacuum pumped. There's a new page for a new app,
3ddipole. It's not so much of an analysis tool as a thing to help spiff up a presentation. Feel free to add your favorite AFNI/SUMA results picture, time-frequency plot, or a clever paragraph or two that'll make the reviewers go "oooh!"
Not so much new to report. The power failure yesterday didn't affect us much, we were just down for a few hours. A reminder: don't schedule slots unless you have confirmed subjects. Use the "hold approval" feature if you just want to reserve the time.
AFNI wizard Bob Cox has modified the command
3dpc
to perform PCA noise/dimension reduction on 3d+time datasets. This is particularly useful for cleaning up SAM sliding window data. A description of how to do this is posted here:
PCA.
Happy Thanksgiving. Tako's /data5 is full, so we're switching to /data6. Symbolic links have been redirected.
The DLP projector is back, and works.
New versions of
samslide and
StockwellDs were uploaded today.
samslide
has some new features (thanks Tyler!) that make it easier to use on regular machines.
StockwellDs
1.4 does normalizations in a more sane way, and the
-B
default was changed (see the usage message).
The DLP projector died. No clue what happened, some electronics failure apparently. It's out for repair.
A minor bug in the
-B
processing of
StockwellDs was fixed. The current version is 1.2.
The final software release from CTF is now online, version 5.4.
Another successful warmup, no problems. Thanks to Slobodan for doing it slowly and carefully. The two new 3T magnets across the hall have no effect on us; our noise levels now are lower than they were before the warmup. We have lots of disk space on the new RAID array, that will last for years.
Scheduled maintenance is going well. The new RAID array has been installed, and Tako is back up. Update: 8/24 Hmm. No, Tako is not back up. We think it might be cabling problems, and are reconfiguring things. Stay tuned. OK, it turns out, you should not mix 320 and 160 speed SCSI devices on the same card or bus.
Matlab 7.3 (R2006b) has been installed on the stimulus computer (under WinXP, not Win98). The Instrumentation Toolbox is now available.
Two new mailing lists of note: the
Biomag list has been moved from the old server at CTF to a Yahoo group, and a new
CTF users group has been formed as well.
The
Stockwell software has been updated to work with fftw3 and numpy, and there's a new command-line tool called
StockwellDs that makes pretty pictures from MEG data.
randpermute has been updated to handle Z-scores such as you might get from 3dWilcoxon (an appropriate test for T-F data).
Kurage died. The server has been replaced, but not everything is working yet. The website is partially restored. Work continues. Update: Most things are working now.
Tako is being upgraded. Host keys have changed. You'll have to edit your .ssh/known_hosts file, and remove the line for tako.
The ongoing construction for the installation of the new magnet continues. We apologize for the sudden power outages and downtime. Meanwhile we are readying a new RAID server, which will have lots of capacity. Also, initial results from head motion correction are in, and they look very good.
Happy new year. It's the year of the pig (wild pig or boar, actually) now. We have installed
VisionEgg on the stimulus computer (Ika). This is a Python package for displaying visual stimuli. Since it's written in Python, it's very easy to use, and free.
A bug in Presentation that caused an access violation on Windows 98 when the scenario tab was clicked has been fixed.
Brainhull 1.7 is now available. This version now uses numpy rather than the old numarray. hull2suma has been updated and a new command to extract fiducials from .mri files, readmrifid.py, has been added.
We installed a new DLP projector. The light curve's rise time with the old projector was something like 30 plus or minus 12 milliseconds, the DLP projector's time is about 5 ms, so visual stimulus timings will be more accurate.
Version 5.2 of the MEG Analysis Software is here! This long awaited update includes the changes necessary for continuous head localization, and also some speedups in the SAM software. Get it here:
CTFSoftwareInstallation. Note that we have not yet switched over to the new Acq, but we will soon, and any datasets collected from that point on will require this new set of tools.
We're up and running.
One of the MEG amplifier cards died. We're having a new one sent out, which should be here Tuesday. We're down until then.
Back from Biomag '06, and our warmup/cooldown cycle went smoothly this time, no broken squids, yay.
Well, time to start on that poster. The MEG lab is very clean now, and we have a new computer, named "isoginchaku", which means "sea anemone" in Japanese.
Biomag is just around the corner; 9 weeks. Is your poster done yet? Mine isn't.
E-prime has been installed on the Stimulus computer.
Happy spring. Cherries, yay! Fred will present SAMerf techniques, Thursday at 2. Also, if your AFNI is more than two weeks old, you are a dinosaur, I have heard.
We've scheduled a
user's group meeting for March 23.
Note: this is two weeks later than the originally scheduled time.
Happy New Year. Presentation has been updated to version 9.90, and the license updated. The user interface has changed a little, but don't panic, everything's still there.
There's a new version of
randpermute
which has a debugging option, and a new example was added to the page.
Check out the new
@auto_tlrc
script in AFNI. It works pretty well. You'll need to use it instead of
adwarp
if you go this route, currently. Remember to run it on the orthogonalized BRIK, and you'll probably want
-no_avoid_eyes
. The
brainhull page has been updated to reflect this and other changes in the current version of AFNI.
Also,
hilbertDs
was updated to work with 5.0 datasets.
There's a new version of
randpermute called
randpermute.py
(it's a Python script). This version is much more capable than the old one; it can do 3dANOVAs as well as 3dttests. It hasn't been tested much on some of the more complex analyses, so please let me know if you have any trouble with it.
Our warmup/cooldown cycle is complete, and the system is again available for recording. We lost another SQUID.
It was one of the MROs, MRO13 to be exact. Oh well, we still have 273 left. Low frequency noise has been reduced. We also got several firmware upgrades, some new electronics, and a few loose screws tightened. We upgraded Kani and Uni, did some housecleaning, and Ika's display can now operate in Dual Head mode (so, for example, it's possible for the subject to see stimuli on one screen, while you see a status display and control the experiment from the other screen). As for Tako, it turns out that /data2's raid array controller was damaged by the power failure. None of the disks will format, and the array can't be rebuilt. The unit is basically dead.
It seems that one of the disks in the raid array was already flaky, and then the power failure pushed another one over the edge, resulting in a failure of the entire array. I'm still trying to figure out exactly what went wrong, but to make a long story short, /data2 is gone.
I have a list of affected directories, but since you all already have hard backups of your data, you shouldn't need this, right? /data2 was only an emergency backup we provided as a convenience. It contained data ranging from 20-Nov-2002 through 31-Aug-2004. We never said we'd keep it forever…
This week is our annual maintenance. We'll warm the system up, and pump on the vacuum for a few days (the maintenance is actually on the vacuum-—the rest of the system doesn't really need anything). In addition we'll be making a few changes around the lab, including OS upgrades on Kani and Uni, and putting a dual-head display card in Ika (the stimulus computer). Update: Tako was accidentally unplugged, and is temporarily off-line while I run consistency checks on the raid arrays, which were under heavy load at the time. /data3 appears fine, but /data2 is still off-line due to errors.
The
Software page now has a copy of
thresholdDetect2
that works with 5.0 datasets. As you may recall, this version features an improved thresholding algorithm that works with inverted signals, proper derivative thresholding, and bandpass smoothing. It's statically linked so no library worries. A few other old tools were added to the
Software page as well.
We're off to Toronto for HBM 2005. Also, on the
ctf2st
page you can find a new accelerated version of the Stockwell transform for Octave, and the
Software page has a link to some Octave code that'll let you use FieldTrip.
The SMI Eye Tracker is now working in interactive mode with Presentation, under Windows XP only. What this means is that your Presentation script can now get real-time eye position data, so for example, you can trigger a trial only after the subject is fixated, or send codes to the MEG system depending on eye position (or pupil diameter). Calibration can also be triggered from Presentation, or you can do it beforehand. Eye position and pupil diameter analog data continue to be available on three ADCs for off-line processing.
The
Ctf2st utility has been modified to run a bit faster. Also, the prestim window for normalization no longer actually has to be 'prestim'.
fred
The
Ctf2st utility now includes a t-test option for use with multiple datasets. The Matlab statistics toolbox is required.
fred
newDs2
has been updated to work with the 5.0 CTF tools.
brainhull
1.6 is available. The
inflateSpheres
and
fiddist
utilities are included, and the webpage and documentation have been updated.
We've updated the
Ctf2st utility to work with version 3 of the FFTW libraries, which is what recent versions of Matlab use, so installation is now nearly painless. The installation instructions have been expanded, and precompiled versions for the NIH Biowulf system are available. Many thanks to the fearless beta testers!