eXTReMe Tracker
Oct 292012
 

As it turns out the if statement in bash isn’t as friendly towards floating point variables as it is for integer and string variables.

First of all the -gt and -lt switches don’t work.Even the unary operators >,<, etc. don’t work. The only way is to do a comparison between the floating point variables using bc and using the logical outout as a comparison string.

a=11.5; b=11.3
compare_result=`echo "$a >$b" | bc`
 if [ $compare_result -gt 0 ]; then
 echo $a
else
echo $b
 fi

 

Sep 192012
 
Simple image compression algorithm using plain FFT computation

FFT2 based image compression

Test code to generate a circular mask that removes the low frequency components from an image.

Step through radius to get the percentage compression.

IM=imread('images_01.jpg');IM=IM(:,:,2); %Select a channel
%
cx=size(IM,2)/2; cy=size(IM,1)/2;
ix=size(IM,2);iy=size(IM,1);r=833;
[x,y]=meshgrid(-(cx-1):(ix-cx),-(cy-1):(iy-cy));
c_mask=((x.^2+y.^2)>r^2);
%
filtIM = fft2(IM).*c_mask;
filtIM = ifft2(filtIM);
IM2=abs(double(IM)-abs(filtIM));
%
x=size(IM,1)*size(IM,2); y=size(find(c_mask==1)); y=y(1);
res=y/x*100;
%
figure(1); 
subplot(2,2,1); imshow(c_mask);
subplot(2,2,2); imagesc(IM2); axis image; axis off;
subplot(2,2,3); imshow(IM); title('Origianl image');
subplot(2,2,4); imagesc(abs(filtIM)); axis image; axis off;
title(sprintf('Percent original: %0.2f',res));
Sep 102012
 

Submitting processing job to a queue

jobs=$scratch/jobs
sub=/lustre/scratch/subjects
# mkdir $jobs
# cp -r $HOME/subjects $scratch/
function run-recon-all() {
cd $scratch
#create submit script for each patient in the subjects directory
do
unset SUBJECTS_DIR
SUBJECTS_DIR=$sub
export SUBJECTS_DIR
cat > $jobs/recon-all-$patient.sh <<EOF
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -N recon-all-$patient
# Set the hard and soft run time limits
#$ -l h_rt=30:00:00,s_rt=29:55:00,vf=2.5G
# set up FreeSurfer environment variables
# mri_convert -oi -os $SUBJECTS_DIR/$patient $SUBJECTS_DIR/$patient.mgz
recon-all -s $patient -all
EOF
done
#submit job script for each patient in the jobs directory to the cluster
pushd $jobs
for script in `ls -1`
do
echo "submitting job $script"
qsub $script
done
popd
}
run-recon-all
Aug 082012
 

Here’s a nifty little script I found.

You need to run it within the directory containing the wma files:

#!/bin/bash

current_directory=$( pwd )

#remove spaces
for i in *.wma; do mv "$i" `echo $i | tr ' ' '_'`; done

#Rip with Mplayer / encode with LAME
for i in *.wma ; do mplayer -vo null -vc dummy -af resample=44100 -ao pcm -ao pcm:waveheader $i && lame -m s audiodump.wav -o $i; done

#convert file names
for i in *.wma; do mv "$i" "`basename "$i" .wma`.mp3"; done

rm audiodump.wav

If you aren’t happy with underscores and want your spaces back, run this on the command line:

for i in `ls *.mp3`; do p=`echo $i | tr '_'  ' '`; mv $i "$p"; done

They will be in the proper format now, and google music compatible.

May 092012
 

If you are going for a complete reinstall of OS and you need to get a list of packages you have at present, so that you can reinstall them after you have installed Linux from scratch, run the following:

#!/bin/bash
sudo dpkg --get-selections | awk '{ ORS=" "; print $1; }' > packagelist.txt

This saves the everything to packagelist.txt. Mind blown!

 

Mar 042012
 

As a prank project we installed a webcam at the front desk of the our office suite, and plugged it into a Linux machine. Then we had a decommissioned 14 inch monitor face the person who was just walking in so that he/she could see themselves in the monitor with absolute clarity. The text beneath said “Smile for the camera”.

This was an one line implementation with VLC. The terminal command for this would be:

vlc --sub-filter "marq{marquee=\$t \$\smile for the camera,color=16776960,position=8}" v4l2:////dev/video0

A false sense of security with some false video surveillance. Of course you can save the stream and turn it into real surveillance.

 

Dec 282011
 

To monitor the instantaneous network usage, execute the ifstat command in bash. You may need to acquire it from a repository if you don’t have it already.

sudo apt-get install ifstat

To display usage on eth0, with a 5 second delay, just once:

ifstat -i eth0 5 1

You can change the number of seconds, and the number of times you want the output displayed. If you don’t specify the count, it will go on forever until you ctrl-c out of it.

So here is a script that displays the download rates in MB/s and upload rates in KB/s every 5 seconds until you hit ctrl-c.

while :
do
# Press ctrl-c to exit
x=`ifstat -i eth0 5 1 | tail -1 | tr '\t' ' '`;  #tail -1 takes the DL and UL speeds in KB/S
x1=`echo $x | cut -d ' ' -f1`; x2=`echo $x | cut -d ' ' -f2`;
x1=$(echo "scale=3; $x1/1024" | bc); # Convert DL rate to MB/S
printf "D: %0.3f MB/s\t U: %0.3f KB/s\n" "$x1" "$x2"
done
Nov 162011
 

On most Linux/Unix based systems, you can save your Matlab figure as a postscript instead of saving it as a png or jpg. One advantage of saving figures in this manner is that you can save multiple images as separate pages on that .ps document, whereas with png/jpg you have to save each image as a separate file.

To print the current image to postscript, all you need to run is:

print(‘-dpsc2′,’filename’);

To have multiple images appended within the postscript document, you need to use the -append switch.

print(‘-dpsc2’, ‘-append’, ‘filename’);

Your output postscript will have the name filename.ps

To convert the postscripts to pdf format, just run the ps2pdf command in the terminal window:

ps2fpdf filename.ps

The output of this would be filename.pdf

And you’re done.

Nov 102011
 

In order to install l1-SPIRiT Compressed Sensing Parallel MRI, we need to have a couple of programs installed – fftw3, lbz2.  Usually you encounter the following error while running build routine in Matlab.

/usr/bin/ld: cannot find -lbz2
collect2: ld returned 1 exit status

sudo apt-get install libbz2-dev

After installing libbz2-dev this error is corrected.

Sep 192011
 

The latest version of Ubuntu is heavily based upon Unity environment. Unfortunately Unity has no track record of playing nice with existing gnome programs. For network applications such as VNC, Unity crashes the program with whole bunch of errors. These crashes are observed occasionally in the Ubuntu 11.04 (Natty Narwhal) release, and most certainly in the latest beta 1 release of Ubuntu 11.10 (Oneiric Ocelot).

If you have gotten comfortable with Ubuntu and want to continue using Gnome as the main environment, you can do so by using Linux Mint 11 (Katya). It has the same repositories as Ubuntu and you can even use the ubuntu-restricted-extras and build-essential packages which lets you obtain some of the fonts, codecs and libraries that Ubuntu fetches for you.

Ubuntu is starting to put more emphasis on making their release into an eye-candy, at the cost of reduced functionality. Having used Ubuntu since Dapper Drake days, its sad to ditch it for another distro. IMO Ubuntu 10.04 was the cleanest distro they put out – things have been going downhill after that. Linux Mint on the other hand picked up at the point when Ubuntu started to go dysfunctional. It has everything that Ubuntu should have been. There isn’t much to write about Mint 11. Its very similar to Ubuntu 10.04, has a newer kernel 2.6.38.xx, clean graphics, and the same repositories as Ubuntu. The transition is very easy, and things look a lot more neater in Mint.

To recap: If you are currently using Ubuntu and are afraid to upgrade to the 11.10 release, your fear is quite justified. Make a backup of your /home folder and go for a clean install of Linux Mint instead. I moved to Mint about a month ago and have had a rather smooth sailing so far.

May 112011
 

Running scripts in serial order on a multi-core machine will take quite a bit of time. If the tasks are repetitive, the command can be run under GNU Parallel.

You can install it on RPM or Debian based distribution from the GNU Parallel repository. Install the binary that fits your flavour of Linux. Please note that even though the latest release of GNU Parallel has a flavour of Linux associated with it, it runs on most of the older AND newer distributions. For instance I was able to install the April 21st 2011 release of amd_64 RPM on a RHEL5 machine, and it ran just fine for that 8 core machine.

After installation you can try it out on a sample directory by running:

ls -d */ | sed ‘s/\///g’ | parallel zip -r -q {}.zip {}

This will recursively zip all the directories within a given folder, in parallel. By default, it will use up the maximum number of cores, but you can check the man pages of parallel to check how to employ N number of processors to run the task in parallel.

ls *.jpg | parallel convert {} -resize 75% -quality 80% {}

If you have imagemagick installed, you could save a whole bunch of space by converting some of the high-res images to a slightly lower resolution. The above example will resize the images to 75% of their original size with 80% quality. The original images will be overwritten by the resize and downsampled ones. While this is running, you can fire up htop in another terminal window to watch all the processors working in parallel.

Apr 142011
 

Assuming the nifti toolbox is in Matlab path, we can get the 91x109x91 mask to have the same dimensions as the normalized images generated with bounding boxes.

If we are making a mask for hippocampus, first we save that mask from WFU Pickatlas. Then to make it 79x95x68 voxels, run the following small script.

x=load_untouch_nii(‘hipp.img’);
x=x.img;xdim=[1:6 86:91]; ydim=[1:6 102:109]; zdim=[1:11 80:91];
origin=[40 57 26]; datatype=16;
x(xdim,:,:)=[]; x(:,ydim,:)=[]; x(:,:,zdim)=[];
nii=make_nii(x, [2 2 2], origin, datatype);
save_nii(nii, ‘boxedhippo.nii’)

We can then use these masks for signal extraction or any further processing.

Mar 302011
 

FSL: flirt is used to compute an intial affine normalization of the T1 weighted images; this is then fed to fnirt to compute the overall transformation. flirt is also used to register the EPI’s to the subject’s structural image. This was then used along with fnirt-s warp in applywarp to normalize the EPIs.

Script for normalizing the T1-weighted structurals to the template:

Registering T1-structural to MNI152
bet my_structural my_betted_structural
 flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat
 fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
 applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural --warp=my_nonlinear_transf --out=my_warped_structural

Registering functional data to MNI152 (via structural scan)

bet my_structural my_betted_structural
 flirt -ref my_betted_structural -in my_functional -dof 7 -omat func2struct.mat
 flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat
 fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
 applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_functional --warp=my_nonlinear_transf --premat=func2struct.mat --out=my_warped_functional