Brain Registration with ANTS Toolkit

In most neuro imaging research it is needed to study specific areas of the brain instead of the wholevolume. For me, as many other researchers, it is very difficult or impossible to locate by hand some specific brain areas. And it is not desired to do conclusions over an area that is not correctly located, because this conclusions will end up corresponding to some other part of the brain. So, is very important to use a good tool for registration. The following papers explain why ANTs is one of the best tools for Brain Registration: 
http://www.mindboggle.info/papers/evaluation_NeuroImage2010/Evaluation_Klein_NeuroImage2010.pdf
http://www.mindboggle.info/papers/evaluation_NeuroImage2009/Evaluation_Klein_NeuroImage2009.pdf
There are no “best parameters”for every registration, it mostly depends on the resolution of the images and the moving and fix spaces as well as many other characteristics. However, I think that there should be some basic recommendations for running a correct corregister, because it would be a waste of time to try on with hundred possibilities for each parameter. As a new ANTs user I struggled a lot trying to find out which could be the best options to be used, because every paper I read would say that the best parameters were different depending each specific situation. But still, for a new user is difficult to guess from zero the best options. So finally, after reading ANTs manual and with personal communication with Dr. Klein, I did a resume that I hope can help as a basis for other people that are learning about ANTs as well.  
The file ants.h that can be found on my web page contains my recommended parameters for doing brain registration from an atlas to a subject's space. It can be executed directly from the command line if you have ANTs installed in your computer. You can find there as well an explanation on how the parameters were chosen. 
Visit www.monicagiraldochica.com (go to 'My PhD Project' > Project Progress > Files)

Touchpad not working AT ALL (Not even in BIOS)

Ok... not having time to post more elaborated stuff... I will go on to give talk about this apparently simple problem...

Today I found out my touchpad was not working. Ok I said... It must be something disabled on the device setup... Nop, it's not. Well... yep, it must be the driver. Uninstall, reboot, re-install, reboot... nop. Ok, it must at any rate, be a Windows problem... let's try Linux... reboot, come on Linux darling... nop, still not working... what the....????

Well, it should work in the BIOS, or there is maybe some option disabled... checking the BIOS... nop, no way... is the hardware broken? did I spill some liquid? did I hit it? no... no that I remember.

Let's google it... config? check, drivers? check, bios? check... ok let's see this post by whiteblade here and... wowwww that actually worked!

The solution: DISCONNECT THE LAPTOP AND TAKE OUT THE BATTERY FOR SOME MINUTES. It should gave time to some part of the memory to discharge, so when out turn it back on, your touchpad will be alive.

Yep, this might not work for everyone... but it did for me and for other people... so this post should help those who are about to start tearing their shirts apart and yelling at the laptop for being so fragile.

Installing Marlin on Ubuntu 11.10

As I got tired of Nautilus lack of certain common features (specially the hability to change from icon view to list view in one click), I decided to install a new explorer on my Ubuntu. The logical option was Marlin, the upgraded version of what was previously called "Elementary Nautilus".

Here are the steps to install it, as I found them here

Type from terminal:


sudo add-apt-repository ppa:elementary-os/daily
sudo add-apt-repository ppa:marlin-devs/marlin-daily
sudo apt-get update
sudo apt-get install marlin


After that, if you are using the gnome-fallback shell (as I am) you can go to the top panel and:
ALT+RIGHT CLICK
Add to Panel...
Custom Application Launcher
Name: Marlin - Command: marlin
And the default Marlin icon will appear.

Click OK and now you can launch Marlin from your top panel.


It worked right away for me and it's MUCH better than the default Nautilus.

Helvetica Fonts

Update 2012-04-25: I've checked this link today and it doesn't seem to be working, I'll post a new one when I find it. Sorry for the inconvenience.

In the last few days I've realized that finding the Helvetica font for free download can be not-so-easy, and actually you could find yourself needing Helvetica for the most unrelated reasons (for me, it was reading an article about mathematics and trying to install a game engine to play Shogi), so I leave here a link the the website where I found the solution:

http://www.safiweb.co.ke/download-helvetica-font-for-free

and, if you want to skip this step, you can just go directly to the downloading site:

http://www.aquadon.com/web/sources/fonts/Helvetica.ttf

Jumping Cursor Problem solved

Well I had this problem of my cursor jumping randomly while I typed, and hadn´t found a good solution, but this guy really found the answer, so if you want you can go to the link and follow the instructions (nevermind the "Content Warning" apparently software and computers are not his major interests, but anyway he found the solution to this problem that seems to affect a lot of people with laptops):

http://slimdave420.blogspot.com/2007/05/jumping-skipping-cursor-problem-solved.html?zx=a3728b21963b8447

Or read the short version:

The problem is that Windows 7 by default uses the PS2 Mouse driver for the touchpad instead of using the proprietary driver. So you should:

1-Find the appropriate driver for your touchpad and download it. (It should be in the manufacturer's website)

2-Uninstall the PS2 mouse driver, BUT DON'T REBOOT!

3-Install the proprietary driver. And reboot.

After this, you should have the touchpad's software, and the problem should be gone. (Anyway, if you have an external mouse, you can use that software to disable the touchpad)

Export/Import Chrome and Chromium history

For a long time I had wanted to do this, because there are so many useful sites that I haven't bookmarked and not even remember the name. So I tried to find a direct tool in Chrome to export and import the history, but unfortunately I couldn't find it. However, I did find this webpage, where they gave me the data I needed to solve it.

The Chrome/Chromium history files (as well as cookies, passwords and others) are stored in this folders:

• Linux: /home/$USER/.config/google-chrome/
• Linux: /home/$USER/.config/chromium/
• Windows Vista (and Win 7): C:\Users\[USERNAME]\AppData\Local\Google\Chrome\
• Windows XP: C:\Documents and Settings\[USERNAME]\Local Settings\Application Data\Google\Chrome\

So all you need to do is backup those folders and then paste them into your new browser if for some reason you have to format or re-install your OS, or just use the same configuration in another computer.

I know there must be a simple way to merge histories from several users, but I just found this today so still haven't devoted time to it. Anyway, I hope someone finds this useful.