eXTReMe Tracker
Jul 312015
 

If gnome-do fails to locate and launch terminal (or gnome-terminal), it is because of a small omission in the gnome-desktop.terminal file.

In terminal run:

locate gnome-desktop.terminal

Once you find that file, open it using nano or gedit with sudo.

sudo nano /usr/share/applications/gnome-terminal.desktop

Search for the line that says:

OnlyShowIn=GNOME;Unity;

Add X-Cinnamon to the end of that line such that it reads.

OnlyShowIn=GNOME;Unity;X-Cinnamon;

That’s it. Once you log out and log back in, terminal will start appearing as one of the search results in gnome-do.

May 272015
 

In Linux Mint 16 and 17, there is a small bug in gnome-do. Well, techincally it is in a file called gnome-terminal.desktop

Searching for terminal in gnome-do in Cinnamon environment gives no results for gnome-terminal. The first entry is usually Printers. This is caused because of an omission in the gnome-terminal.desktop file.

Open terminal by searching through start menu:

locate gnome-terminal.desktop

You will usually find it at: /usr/share/applications/gnome-terminal.desktop

sudo nano /usr/share/applications/gnome-terminal.desktop

Find the line that says:

OnlyShowIn=GNOME;Unity;

To that list add X-Cinnamon so it will read.

OnlyShowIn=X-Cinnamon;GNOME;Unity;

Save the file and log out. Once you login again, terminal should appear on top of Gnome-do search as soon as you type t.

May 042015
 

Found a 5-leaf clover in my garden this morning. Definitely a step up from a four leaf one.

 

Apr 232015
 
Dining Area Kitchen Kitchen Dining Area Porch Backyard Backyard From the backyard Porch Kitchen Living and Kitchen capecod012 Staircase Master Bedroom Guest Bedroom Guest Bedroom Front Landing Living Area Staircase Staircase Garage Garage Garage Garage Basement - Den and Bedroom Basement den Basement den Below the staircase Two car garage Some sectioned out places in yard From the edge From the edge Guest Bath Guest Bath Bath Bath Bath Master Bed Master Bed Master Bed Door Street View Street View Front Door
Dining Area
Dec 222014
 

The purpose is to to convert a 3-dimensional image file which contains X,Y and the dimensions containing RGB values to a 2D image file in grayscale. It can be done in linux command line using imagemagick.

convert <img_in> -set colorspace Gray -separate -average <img_out>

The resulting image is a 2D image generated by averaging the R,G,B arrays.

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.

Sep 162014
 

Every once in a while as you are trying to make a .iso file from a DVD using Brasero, you might get an error saying that couldn’t retrieve the keys because of libdvdscc2.

An alternative to that is a command line tool called dvdbackup which first needs to be installed

sudo apt-get install dvdbackup

After installing that program, you can make backup of your entire dvd, unfortunately not an .iso. You can create an iso from the folder that gets generated once you backup the dvd using dvdbackup. To create a backup, open your terminal and run:

 dvdbackup -M -i /path/to/dvd/  -n Title_For_Backup -o /path/to/output/directory

To get help of dvdbackup you simply have to type in dvdbackup at the terminal.