Changing variable names based on a string

Hi all,

I am trying to do some basic imaging processing where I want a script to run through different ROIs on each hemisphere of the brain. Right now I have to run a script manually with each file name (RightPLIC). Is there anyway to code file names with two separate editable strings? i.e. ('hemisphere''ROItarget')

So that I don't have to manually change each line each time I run the code? In linux I typically use {$fname}, but that won't work here...

Thanks in advance for any help!

Below is an example of what I'm talking about. I want to be able to just update "right" or "M1" or "PLIC" more quickly.

% files needed to do pde tracking seedfile = [dirname, 'RightPLIC']; % seed targetfile = [dirname, 'RightM1_ACPC_DTI_space']; % target

    maskfile = [dirname, 'dti.moco.bet '];        
    sidemaskfile = [dirname, 'right_mask'];  % this will be combined with anatomical mask

    % name of output file: nifti
    outputfile = 'RightM1_ACPC.count';
    File = 'RightM1_ACPC.count.nii.gz';

Answer 1

[Nathan]

Kelsey,

I would check out strcat: http://www.mathworks.com/help/matlab/ref/strcat.html

You could have a conditional block at the top of your code and you could change the value of say n and switch the value of the a string based on this.

n=1;
if n==1,
    String1 = 'Right';
    String2 = 'M1';
elseif n==2,
    String = 'option2';
elseif n==3,
    String = 'option3';
else
    Error('Selection is not a valid option');
end

Then you can change your code in some form like:

    % name of output file: nifti
    outputfile = strcat(String1, String2, '_', 'ACPC.count');
    File = strcat(String1, String2, '_', 'ACPC.count.nii.gz');

This method works great, just not sure if I percived exactly what parts needed to be dynamicallly changible. Let me know if you have any questions about this method.

[Kelsey]

Thank you so much Nathan! This worked beautifully!

Answer 2

[Ahmet Cecen]

Use eval alongside strcat and num2str.

Answer 3

[Joseph Cheng]

Sightly confused on what you're trying to do but here is my attempt.

STR = 'Right'; %or M1 or PLIC

% files needed to do pde tracking 
  seedfile = [dirname, STR, 'PLIC'];  % seed 
  targetfile = [dirname, STR, 'M1_ACPC_DTI_space']; % target

    maskfile = [dirname, 'dti.moco.bet '];        
    sidemaskfile = [dirname, STR, '_mask'];  % this will be combined with anatomical mask

% name of output file: nifti
  outputfile = [STR, 'M1_ACPC.count'];
  File = [STR, 'M1_ACPC.count.nii.gz';

Since these are all String arrays you can concatenate them with each other like you were already doing. Since i couldn't figure out based on your example of the target file and output file having RightM1 i left it in there. you could possibly edit this with a switch/case statement so depending on what the edit string is you can get two string substitution variables to make 'RightM1' instead of just right.

 %air coding so pardon any errors
  type = 'Right'
  switch type
  case 'right'
     STR1 = 'Right'
     STR2 = 'RightM1'
  case 'M1'
     STR1 = _)___
     STR2=_____
  case 'PLIC'
  end

same stuff above but use STR1 or STR2 depending on which one fits.

Additionally if your files are named in a particular way you could write this to do it automatically and detect which strings to update.