eXTReMe Tracker
Dec 152014
 

Converting nifti files to dicom using nifti toolbox in matlab

clear; clc;
 addpath('/usr/local/matlab/toolbox/niftitools');
 subjectdir='/media/storage/SPECT_mapping/bbobby';
 cd(subjectdir);
 [dicomfile, dicompath] = uigetfile('*.dcm','Select DICOM header for metadata');
 metadata = dicominfo(fullfile(dicompath, dicomfile));
 metadataISAS=metadata; metadataMPR=metadata; metadataFUS=metadata;
 
 metadataMPR.SeriesDescription = 'SAG_MPRAGE_T1_Recon'; metadataMPR.SeriesNumber = 1;
 metadataISAS.SeriesDescription = 'ISAS Hyperperfusion'; metadataISAS.SeriesNumber = 2;
 metadataFUS.SeriesDescription = 'MPRAGE ISAS Fusion'; metadataFUS.SeriesNumber = 3;
 
 cd(subjectdir);
 isas = uigetfile('hyper*.nii','Select hyperpefusion file');
 structural = uigetfile('mprage*.nii','Select MPRAGE');
 
 isas = load_untouch_nii(isas); isas = isas.img; isas = int16(isas);
 structural = load_untouch_nii(structural); structural = structural.img;
 
 display('... Merging Hyperperfusion and MPRAGE');
 
 merged = structural;
 merged(isas>0) = max(max(max(structural)))+10;
 
 display('... Finished Merging')
 
 isasdir = fullfile(subjectdir,'isas');
 if exist(isasdir) ~= 7
     mkdir(isasdir);
     mkdir(fullfile(isasdir,'SPECT_ISAS')); spectdir = fullfile(isasdir,'SPECT_ISAS');
     mkdir(fullfile(isasdir,'structural')); structdir = fullfile(isasdir,'structural');
     mkdir(fullfile(isasdir,'fusion')); fusiondir = fullfile(isasdir,'fusion');
 end
 
 cd(isasdir);
 
 % dicomwrite(reshape(x4,[170,256,1,256]), 'SPECT_ISAS.dcm', metadata, 'CreateMode', 'copy');
 display('... Creating DICOMS');
 
 for slicenum = 1:size(isas,1)
     
     cd(spectdir); metadataISAS.InstanceNumber = slicenum;
     dicomwrite(fliplr(rot90(squeeze(isas(slicenum,:,:)))), sprintf('SPECT_ISAS_%03d.dcm',slicenum), metadataISAS, 'CreateMode', 'copy');
     
     cd(structdir); metadataMPR.InstanceNumber = slicenum;
     dicomwrite(fliplr(rot90(squeeze(structural(slicenum,:,:)))), sprintf('structural_%03d.dcm',slicenum), metadataMPR, 'CreateMode', 'copy');
     
     cd(fusiondir); metadataFUS.InstanceNumber = slicenum;
     dicomwrite(fliplr(rot90(squeeze(merged(slicenum,:,:)))), sprintf('FUSION_MPR_ISAS_%03d.dcm',slicenum), metadataFUS, 'CreateMode', 'copy');
     
     display(sprintf('... Creating slice %d',slicenum))
 end
 
 cd(subjectdir);
Oct 232014
 

To compute a transpose of an input file, i.e. converting columns to rows and rows to column using bash, you can accomplish that using awk and while loop.

#!/bin/bash
cols=`cat $1 | head -1 | wc -w`;
for i in $(seq 1 $cols);
do
awk -v "n=$i" '{print $n}' $1 | tr '\n' ' ';  # variable column output
printf "\n";
done

This example uses a variable to output a specific column from the input.

awk -v "n=$variable" '{print $n} ' input.txt

Will pass the variable to n and the nth column gets printed from input file.

Aug 212013
 

If the gnome/mate/cinnamon session becomes unresponsive, you can use the Ctrl+Alt+F1 key sequence to get to shell mode. Once there,  you can login and run the following command to end the graphical session:

sudo pkill -KILL -u USER_NAME
Jan 112013
 

To get the stock quotes for NYSE listings create some file named stockval and add it to your PATH.

Then gedit the file with the text:

#!/bin/bash

p=`printf "curl -s 'http://download.finance.yahoo.com/d/quotes.csv?s=$1&f=l1'"`
price=`eval $p`;
echo $price

stock_quote_ticker

 

 

 

 

 

 

 

 

 

 

Make that file executable

chmod +x stockval

Close out, and open a terminal. If you have the path correctly configured, execute the stockval command using the company symbol as an argument and it returns the stock price on the line below.

stockval goog

732.15 << output
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.