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Summary: Another fun show includes our guest Gordon Sinclair, who helps us learn about the value of Mint and discusses a plethora of other topics

HIS is our eighth episode. Gordon, Tim, and Roy speak about a range of issues with special focus on Linux Mint upon its new release, called/dubbed “Julia”. While not talking about Mint we also go through the differences between Windows and GNU/Linux in general. At the end we discuss some of the latest bad news that Windows Phone 7 needs to cope with (storage problems). Tim’s site, OpenBytes, will soon share some links about the topics we cover. Gordon’s good site can be used to keep track of his work, including some projects he tells us about in advance (it is at the very end of the show).

Today’s show ends with our theme song from Tom Smith. We hope you will join us for future shows and spread the word if you enjoy this show. Also consider subscribing to the show via the RSS feed. If you have an Identi.ca account, consider subscribing to TechBytes in order to keep up to date. We have begun listing past shows at the bottom of each post, based on listeners’ feedback that suggested this.

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Summary: A daily news roundup with special focus on an easy-to-debunk GNU/Linux ‘article’ from The Economist

HIS is the seventh episode, which Tim and Roy keep short to obey requests from regular listeners of the show. Our leading story today is a fun FUD piece from The Economist, which is talked about for the first 10 minutes or so. Tim’s site, OpenBytes, will share some links about that.

Today we play no special song and instead revert back to our default one from Tom Smith. We hope you will join us for next week’s shows, which will be more packed with stories.

As always, if you enjoy this show, please consider recommending it to others and consider subscribing to the show via the RSS feed. If you have an Identi.ca account, consider subscribing to TechBytes in order to keep up to date.

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Keywords: Open Access; Free software; Cardiac cine-MRI; Brain; Segmentation; Tagging; Cardiac deformation analysis

Overview

his informal post presents a quick survey of what’s available for one to find when it comes to heart tagging downloads (without having to go through radiologists and all sorts of burdensome forms). It is a problem I’ve been tackling recently and I would like to share my findings to make life easier for other scientists who find themselves in the same situation.

Some Background Information

WEEK OR SO ago I decided to share information about the availability of datasets for researchers. When faced with the problem of looking for, say, ‘”tagged MR” images heart download dicom’ (and a lot of searching around this phrase) I was surprised to find that almost nobody publicly shared or made discoverable a dataset one can use for research purposes. In order to simplify the task for others who find themselves in a similar situation, several days ago I wrote about my intentions to make a sort of summary [1, 2].

As a bit of background, our original plan was to write and implement special protocols with engineers at the MRI scanner, as part of the research effort by which special types of data are obtained for a novel approach to be tested. This is explained in a paper I’ll put up in the site pretty soon.

At the moment, due to particular constraints, we are working on analysis of sequences of tagged data. This obviously requires not just MR images of the heart but also sequences and these, preferably sequences that must have particular types of tags which a radiologist would use. Data can be acquired/sliced from different angles and obtained from any subject/patient at the hospital^*, but for this particular approach that we test (to be covered in a separate post) this is rather irrelevant as we want it to be applicable regardless of factors like angles, subjects, and potentially their atrophies.

Resources

SourceForge hosts quite a few MRI-related software projects which are free/libre and thus of value to MRI-based research (our methods and data should be made freely accessible for independent validation). One of these projects is the cardiac MR toolbox for Matlab, which may also be fully compatible with Octave (free/libre software). “The cardiac MR (CMR) toolbox for Matlab,” explains the official Web page, “provides tools for image registration, perfusion analysis, segmentation, and image reconstruction from sparsely sampled data.” Here is the alternative project homepage. It states:

This is the Cardiac MR toolbox for Matlab project (“cmr-toolbox”)

This project was registered on SourceForge.net on Mar 29, 2010, and is described by the project team as follows:
The cardiac MR (CMR) toolbox for Matlab provides tools for image registration, perfusion analysis, segmentation, and image reconstruction from sparsely sampled data.”

For brain MRI there is the RESCUE brain MRI segmentation project. It is not yet available, but it soon will be. Its author states: “RESCUE will be made available after publication of the PhD thesis of James Withers (Uni of Edinburgh, UK). The first version of the package will initially include super-resolution, thin structure detection, and partial volume estimation components.”

Of course, one can get brain datasets from the rather famous BrainWeb (more here) and some more data resides in my site, including a sample set of images and some DICOM-formatted data of my own brain (acquired at Hope Hospital for a colleague’s experiment back in 2005).

Moving on to the heart, there is a cardiac MRI dataset which is not terribly useful because almost everything is encoded and stored in MATLAB format and may therefore require some loaders that are proprietary (Octave does not cope so well with those).

There is another project called inTag and this Web pageoffers a a look at what’s done there. Another page offers a look at how it’s used. It is “a software to calculate, display and analyze myocardial strains and intra-myocardial mechanics from cardiac MR images with a tagging pattern.”

The dependencies on proprietary software are unfortunate though. As the page puts it: “After a preliminary prototyping step in Matlab ®, InTag is now available as a plugin in OsiriX, the advanced open-source image processing software. It benefits of all its unique capabilities for navigation, visualisation of multimodality and multidimensional images, and data management.”

This requires OsiriX, which is Free/open source software, but only for Macs, which is not terribly useful then. Here is some tagging from this software package called inTag. It’s just a group of some very low-resolution images in DICOM format (small and not so useful at all).

Another dataset which I find odd (not because it’s made available just in very low resolution but because there is something odd in orientation) comes from New Zealand. Images are said to be available for download, but they are all encoded as AVI-formatted slanted videos and also compressed. The only one set with tagging data is not too helpful, either. The page states that “The Auckland MRI Research group has agreed to make freely available 256×256 JPEG images and image orientation information for download. In addition the Auckland MRI Research group has also agreed to make freely available the cines in AVI format”. What’s listed in the page as an overview is as follows:

All 119 T1-weighted jpeg images
akld-mrirg-atlas-jpegs.zip (4.33MB)
12 Long axis trueFisp avi movies
akld-mrirg-cines-truefisp-long.zip (21.76MB)
1-15 Short axis trueFisp avi movies
akld-mrirg-cines-truefisp-short-a.zip (25.32MB)
16-30 Short axis trueFisp avi movies
akld-mrirg-cines-truefisp-short-b.zip (28.61MB)
3 Aorta and 1 RVOT trueFisp avi movies
akld-mrirg-cines-truefisp-aorta-rvot.zip (7.42MB)
11 Long axis and 15 Short axis tagged avi movies
akld-mrirg-cines-tagging.zip (26.46MB)
Aorta(2) / Right(2) and Left(2) Pulmonary arteries(4) phase contrast avi
movies akld-mrirg-cines-phasecontrast.zip (10.34MB)

Those sets are not tagged except akld-mrirg-cines-tagging.zip. There is also no data from the Cincinnati Children’s Hospital Medical Center, which shows up among many search results. Search for data has proven to be quite fruitless, generally speaking.

Eventually I used data which I acquired from someone’s thesis frame by frame, only to be seen as a temporary solution until data comes from a group that keeps it for internal use. The conclusion is that the Web is generally a poor resource for such data, especially if tagging is a requirement. If someone knows of an exception, please comment below.

Some References

On this fruitless pursuit for data the following references were seen as potentially relevant (publication names mostly omitted as it’s easy to search by title).

DN Metaxas, “A Segmentation and Tracking System for 4D Cardiac Tagged MR Images,” 2008.

L Axel, “Tagged MRI-Based Studies of Cardiac Function,” Computerized Medical Imaging and Graphics, Volume 29, Issue 8, December 2005, Pages 607-616, 2003.

D Goksel, “Towards rapid screening of tagged MR images of the heart,” 2002.

NF Osman, “Angle Images for Measuring Heart Motion from Tagged MRI.”

L Axel, “An Integrated Program for 2-D and 3-D Analysis of Heart Wall…,” 2002.

Y. Chenounea, “Segmentation of cardiac cine-MR images and myocardial deformation assessment using level set methods,” 2005.

(Abstract: “In this paper, we present an original method to assess the deformations of the left ventricular myocardium on cardiac cine-MRI. First, a segmentation process, based on a level set method is directly applied on a 2D+t dataset to detect endocardial contours. Second, the successive segmented contours are matched using a procedure of global alignment, followed by a morphing process based on a level set approach. Finally, local measurements of myocardial deformations are derived from the previously determined matched contours. The validation step is realized by comparing our results to the measurements achieved on the same patients by an expert using the semi-automated HARP reference method on tagged MR images.)
____
^* Some are too blurry and others paint areas with blood presence black, which help isolate the boundaries of important structures for subsequent analysis.

few days ago I started working with Fedora 14. So far, so good, at least as far as the desktop machine goes (a laptop is another story and Kubuntu runs fine on another desktop). Something has just happened in Fedora which never happened to me before. Kate (an editor) got stuck and its memory (RAM) consumption went up through the roof to over 1.5 GB, so obviously it froze the system for a while. The process needed to be forcibly killed.

Now, it’s not entirely clear what happened there (maybe a program bug), but this is unusual and it looks bad for Fedora or for KDE (or the combination in Fedora 14 KDE spin). What did happen is that SELinux came up with an error implying that it stood in Kate’s way and maybe it’s partly responsible for this type of behaviour. It yielded the following error, implying that it was trying to help when in fact it seemed like it only stood in the way.

Summary:

SELinux is preventing /usr/bin/kate (deleted) “mmap_zero” access on <Unknown>.

Detailed Description:

SELinux denied access requested by kate. The current boolean settings do not
allow this access. If you have not setup kate to require this access this may
signal an intrusion attempt. If you do intend this access you need to change the
booleans on this system to allow the access.

Allowing Access:

Confined processes can be configured to run requiring different access, SELinux
provides booleans to allow you to turn on/off access as needed. The boolean
mmap_low_allowed is set incorrectly.
Boolean Description:
Control the ability to mmap a low area of the address space, as configured by
/proc/sys/kernel/mmap_min_addr.

Fix Command:

# setsebool -P mmap_low_allowed 1

Additional Information:

Source Context unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1
023
Target Context unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1
023
Target Objects None [ memprotect ]
Source kate
Source Path /usr/bin/kate (deleted)
Port &ltUnknown>
Host blueberry
Source RPM Packages
Target RPM Packages
Policy RPM selinux-policy-3.9.7-3.fc14
Selinux Enabled True
Policy Type targeted
Enforcing Mode Enforcing
Plugin Name catchall_boolean
Host Name blueberry
Platform Linux blueberry 2.6.35.6-45.fc14.i686 #1 SMP Mon
Oct 18 23:56:17 UTC 2010 i686 i686
Alert Count 112
First Seen Sun 14 Nov 2010 09:35:01 AM GMT
Last Seen Sun 14 Nov 2010 09:35:17 AM GMT
Local ID 4d9759c9-e672-475d-bf61-151d1688909a
Line Numbers

Raw Audit Messages

node=blueberry type=AVC msg=audit(1289727317.378:856): avc: denied { mmap_zero } for pid=1880 comm=”kate” scontext=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 tcontext=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 tclass=memprotect

node=blueberry type=SYSCALL msg=audit(1289727317.378:856): arch=40000003 syscall=192 success=no exit=-13 a0=0 a1=100000 a2=0 a3=4022 items=0 ppid=1629 pid=1880 auid=500 uid=500 gid=500 euid=500 suid=500 fsuid=500 egid=500 sgid=500 fsgid=500 tty=(none) ses=1 comm=”kate” exe=2F7573722F62696E2F6B617465202864656C6574656429 subj=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 key=(null)

For years I’ve been working with no data loss, but this time I had to revert back to a previously-saved version of a document I worked on and then rewrite bits of it. Perhaps I had enough confidence in the system to only hit save (CTRL+S) once in a very long time. This experience has taught me to save my work more often but more importantly it showed that Fedora can act rather bizarrely where Kubuntu never did. As a result of this behaviour I was unable to save my work. SELinux implies there was an “attack” on the system, but obviously there was not.

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Summary: A weekly roundup with special focus on hands-on experience and impressions of the latest major release of GNU/Linux, namely Fedora 14

HIS is the sixth episode, which has just been recorded by Tim and Roy. This was done right after today’s testing of Fedora and Fusion 14. I installed it permanently on 2 boxes, whereas Tim tried Fusion on his side and, as usual, his site OpenBytes has some show notes. As we’ve both had a chance to test it on some machines, we may also post detailed reviews soon (c.f. [cref 41364 our first show], which was a Fedora 14 special that covered Fusion too).

To summarise my experience in textual form, it was a KDE-only experience and an especially wonderful one. Having just installed Fedora 14 on another box and encountered very few difficulties (ClaudioM and other people who spoke back to me were generally happy with it as well, only with minor pet peeves). I spent many hours on it, getting a feel for what’s installed, what works, and what is harder to use. Among the installations, the first, on a desktop, went smoothly, but the second, a notebook, had the same issue as Mandriva had with it (built-in microphone not detected, so external one needed). There is a lot to be said about the startup speed and about Plasma, which has nonetheless given me a hard time today. Plasma-desktop in KDE (4.5) is very pleasant and it provides a good-looking desktop and brilliant experience. Unfortunately it decided to repeatedly crash on the laptop and it’s possibly simple to resolve (will retry tomorrow).

As time goes on, TechBytes manages to become more focused, concise, and also incorporate a logical structure which makes it easier to follow. We also intend to end every show with a song from now on. This show closes with “On My Kees” from Aqualung (freely obtainable via SXSW 2009 Showcasing Artists).

If you wish to be on the show or know someone who ought to be on the show, please let us know. Marti spoke with us for a long time today, but we are trying to sort out recording difficulties which will hopefully be overcome soon. We are eager to have him on a future show.

As always, if you enjoy this show, please consider recommending it to others and consider subscribing to the show via the RSS feed. If you have an Identi.ca account, consider subscribing to TechBytes in order to keep up to date.

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Summary: This is the longest show so far and it covers a wide range of topics with no specific item of focus

HIS is the fifth episode, which was recorded last night. OpenBytes has some show notes and the structure of this show has improved somewhat (the show is still not scripted in any way, as a matter of preference).

This show closes with “Axxo” from “Binaerpilot” (binaerpilot.no) (album name is “Nordland”).

If you wish to be on the show or know someone who ought to be on the show, please let us know. As always, if you enjoy this show, please consider recommending it to others and consider subscribing to the show via the RSS feed. If you have an Identi.ca account, consider subscribing to TechBytes in order to keep up to date.

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intend to publish a long overview of Web resources for tagged data. In the mean time, based on the excellent Web page of Zhen Qian I have managed to piece together something for people to play with. From his thesis [PDF] I’ve extracted a series of 6 frames that I’ve produced the above videos from. I’m hoping to receive high-resolution data to test code with, probably later this month. If the data can be legally shared, I will try to ensure people can get it from this Web site so that getting things done becomes less of an unnecessary ordeal to others.