eXTReMe Tracker
Jan 062016
 

For the past several releases the option of opening something in terminal by right clicking on the desktop, a file or a folder has been missing in MATE environment of Linux mint. This has been set by default. However you can enable that functionality by installing a package called caja-open-terminal.

sudo apt-get install caja-open-terminal

After installing the package, you will have “Open in terminal” as one of the options in the context menu when you right click on icons or certain locations.

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.

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 252013
 

Before making any modification to any files, first create a backup of smb.conf file

sudo cp /etc/samba/smb.conf  /etc/samba/smb.conf.bak

The open the configuration file for editing:

sudo gedit /etc/samba/smb.conf

In the section identified as Share Definitions, insert this piece of code. The path string should be the path for folder you will be sharing. If you want others to have the ability to write to that directory –

sudo mkdir -p /path/to/shared/folder
sudo chown nobody.nogroup /path/to/shared/folder
[share]
    comment = Ubuntu File Server Share
    path = /path/to/shared/folder
    browsable = yes
    guest ok = no
    read only = no
    create mask = 0755

Once the configuration file has been saved, its time to restart the samba daemon

sudo restart smbd
sudo restart nmbd

Once the samba daemon has restarted, you need to add a list of users who can access samba folder.

sudo smbpasswd -a username

To access this directory from windows, open My Computer -> Tools -> Map Network Drive

Folder address for this share would be:

\\ip_address_of_your_server\share

NOTE: The folder is called share in the share definition. You can call it something else and edit the parameters based on the chosen share name.If you want to have access to this folder each time, make sure to save the password and check that option to reconnect at login.

 

 

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