ImageJ and Volume Measurement

In which I describe the complexities of analysing 3D images...

3D image analysis just seems to be one of those things that is harder to do than I'd like it to be.

Before starting it is worth pointing out that with MRI you can acquire volumes in two ways - traditional 2D with multiple slices or a 3D scan. As far as this blog post is concerned these are the same.*

A common measure in clinical MRI is the volume of an organ or part of an organ. After all when someone has brain cancer - "How big is the tumour?" can be a very important question. Here are my experiences of trying to measure volumes on MRI images.

*There are differences between these two methods of acquisition but that would require a whole blog post on it's own.

(Just over) A fortnight of Windows 8

In which I review the Windows 8 experience so far...

So I installed Windows 8 about two and a half weeks ago. In brief - it's a slightly improved version of Windows 7 with a few quirks and a start-up screen that require getting used to. In more detail:

Gentoo 64-bit

So guess what I was up to last night - yes that's right, installing Gentoo.

This was my first time installing Gentoo on 64-bit architecture - the important specs are below:

  • Intel Core i7 2600k Processor (Sandy Bridge - important later)
  • 8 GB DDR3 RAM
  • Asus P8Z68-V PRO/GEN3 Motherboard
  • 250 GB HDD (well 250 GB partition out of the 4 TB in my machine)
  • Nvidia GeForce GTS 450 GPU
  • Blu-Ray recorder drive

Also worth noting that this is a dual boot with Windows 7.

[WARNING - If you're not interested in Linux or computer geekery I expect you will find the rest of this post boring]

I followed the Gentoo documentation found here: http://www.gentoo.org/doc/en/handbook/ I will be noting any differences between that guide and my install here.

Choosing the Right Installation Medium

I downloaded the LiveCD and used that as my initial Linux environment for installing from.

Configuring your Network

All done through DHCP.

Preparing the Disks

I used the standard layout of boot, swap and root partitions but on /dev/sdb2 to /dev/sdb4 because of my dual booting. I set my swap partition to 20 GB following advice I found online. Then annoyingly the LiveCD made me reboot in order to write the changes. The I used the standard filesystems.

Installing the Gentoo Installation Files

The -march option in CFLAGS needs to be native or corei7-avx because of the Sandy Bridge architecture. I used MAKEOPTS="-j5" as it's a quad core processor.

Installing the Gentoo Base System

I selected the default amd64 profile. I set up my USE flags with KDE in mind so -gnome and -gtk were used. I also added the bluray flag.

Configuring the Kernel

I mostly followed the guide but later I had to come back and recompile without some Nvidia options: http://www.gentoo.org/doc/en/nvidia-guide.xml#doc_chap3

Configuring your System

I always set my hostname to be the name of a famous fictional computer - this time I went for Ozymandias (http://en.wikipedia.org/wiki/List_of_fictional_computers#1990s)

I set my locale to be en_GB.UTF-8.

Installing Necessary System Tools

I chose to get syslog-ng, vixie-cron, mlocate, dhcpcd and ppp.

Configuring the Bootloader

I used GRUB and followed the standard set-up except for a timeout of 10 seconds and replacing Windows XP with Windows 7. I also had to ensure to make the boot device hd1,1 and root=/dev/sdb4.

Finalizing your Gentoo Installation

I made my user with nearly all the groups (N.B. games doesn't work - is it depreciated?)

Where to go from here?

By the time I left for work this morning I had also emerged X-org and KDE 4.8.3 and had managed to get startx to not crash while going to a black screen. I'm going to have to work on my xorg.conf this evening and hopefully I'll get a working one running. This will be useful as Googling doesn't currently give a working one for my 42" TV and graphics card via HDMI. I hope people might find that useful :)

Tom out!

P.S. http://www.gentoo.org/