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t_initVistaSession

Illustrates how to initialize a mrVista session with functional MRI data using sample data set erniePRF

Dependencies: Remote Data Toolbox

This tutorial is part of a sequence. Run t_initAnatomyFromFreesurfer prior to running this tutorial.

Summary

- Download erniePRF sample data set - Create new folder, and move EPI and inplane files there - Specify session parameters - Initialize and visualize

Tested 07/21/2016 - MATLAB r2015a, Mac OS 10.11.6

See also: t_initAnatomyFromFreesurfer

Winawer lab (NYU)

Contents

Download ernie raw MRI data 

% Remember where we are
curdir = pwd();

% If we find the directory, do not bother unzipping again
forceOverwrite = true;


% Get it
erniePRFOrig = mrtInstallSampleData('functional', 'erniePRF', [], forceOverwrite);

Organize functional data 

% Create a new directory in 'scratch' for the tutorial
erniePathTemp = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF');

% Navigate and create a directory
cd(erniePathTemp)


% Set up Raw data file directory
mkdir Raw;


% These are the EPI and inplane files downloaded with the pRF sample data
fname{1} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI01.nii.gz');
fname{2} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI02.nii.gz');
fname{3} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI03.nii.gz');
fname{4} = fullfile(erniePRFOrig, 'Raw', 'ErnieInplane.nii.gz');


% Move the files from the downloaded directory to the new, clear directory
for ii = 1:length(fname)
copyfile(fname{ii}, fullfile(erniePathTemp, 'Raw'));
end

Warning: Directory already exists.

Initialize a vistasoft session 

% These files have been copied to the scratch directory. Use local paths.
epiFile{1}     = fullfile('Raw','Ernie_EPI01.nii.gz');
epiFile{2}     = fullfile('Raw','Ernie_EPI02.nii.gz');
epiFile{3}     = fullfile('Raw','Ernie_EPI03.nii.gz');
inplaneFile    = fullfile('Raw','ErnieInplane.nii.gz');
anatFile       = fullfile('3DAnatomy', 't1.nii.gz');

% Generate the expected generic params structure
params = mrInitDefaultParams;


% And insert the required parameters:
params.inplane      = inplaneFile;
params.functionals  = epiFile;
params.sessionDir   = erniePathTemp;


% Specify some optional parameters
%       3D volume anatomy (originally from freesurfer)
params.vAnatomy     = anatFile;
%       Drop the first 8 volumes in each scan, keep remaining volumes
params.keepFrames   = [8 -1; 8 -1; 8 -1];
%       Subject ID. For most labs, it is probably safest to use an
%       anonymized coding scheme
params.subject      = 'Ernie';
%       Name for each of the three scans
params.annotations = {'PRF 1', 'PRF 2', 'PRF 3'};


% Do the initialization:
ok = mrInit(params);


% Open a graphical user interface to ensure that we succeeded
vw = mrVista('inplane');

***** [mrInit] Initializing Session erniePRF ***** (21-Jul-2016 10:06:23)
[niftiCheckQto] NIFTI header origin is at or outside the image volume.
[niftiCheckQto] Origin to the image center [52.000,40.000,12.000] pix.
[niftiCheckQto] NIFTI header origin is at or outside the image volume.
[niftiCheckQto] Origin to the image center [52.000,40.000,12.000] pix.
[niftiCheckQto] NIFTI header origin is at or outside the image volume.
[niftiCheckQto] Origin to the image center [52.000,40.000,12.000] pix.
[mrInit]: Finished initializing mrVista session. 	(21-Jul-2016 10:06:25)
[niftiCheckQto] NIFTI header origin is at or outside the image volume.
[niftiCheckQto] Origin to the image center [80.000,104.000,12.000] pix.
***** [mrInit] Finished Initializing Session erniePRF (21-Jul-2016 10:06:25)*****
Initializing Inplane view
Attaching menus
[niftiCheckQto] NIFTI header origin is at or outside the image volume.
[niftiCheckQto] Origin to the image center [80.000,104.000,12.000] pix.
Attaching popup menus
Attaching sliders
Could not find /Users/jonathanwinawer/matlab/git/vistasoft/local/scratch/erniePRF/Inplane/userPrefs.mat
Done initializing Inplane view

Clean up

close(viewGet(vw, 'figure number'); mrvCleanWorkspace cd(curdir)


Published with MATLAB® R2015a

<!--
SOURCE BEGIN

%% t_initVistaSession % % Illustrates how to initialize a mrVista session with functional MRI data % using sample data set % % Dependencies: % Remote Data Toolbox % % This tutorial is part of a sequence. Run % t_initAnatomyFromFreesurfer % prior to running this tutorial. % % Summary % % - Download sample data set % - Create new folder, and move EPI and inplane files there % - Specify session parameters % - Initialize and visualize % % Tested 07/21/2016 - MATLAB r2015a, Mac OS 10.11.6 % % See also: t_initAnatomyFromFreesurfer % % Winawer lab (NYU)

%% Download ernie raw MRI data

% Remember where we are curdir = pwd();

% If we find the directory, do not bother unzipping again forceOverwrite = true;

% Get it erniePRFOrig = mrtInstallSampleData('functional', 'erniePRF', [], forceOverwrite);

%% Organize functional data

% Create a new directory in 'scratch' for the tutorial erniePathTemp = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF');

% Navigate and create a directory cd(erniePathTemp)

% Set up Raw data file directory mkdir Raw;

% These are the EPI and inplane files downloaded with the pRF sample data fname{1} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI01.nii.gz'); fname{2} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI02.nii.gz'); fname{3} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI03.nii.gz'); fname{4} = fullfile(erniePRFOrig, 'Raw', 'ErnieInplane.nii.gz');

% Move the files from the downloaded directory to the new, clear directory for ii = 1:length(fname) copyfile(fname{ii}, fullfile(erniePathTemp, 'Raw'));
end

%% Initialize a vistasoft session

% These files have been copied to the scratch directory. Use local paths. epiFile{1} = fullfile('Raw','Ernie_EPI01.nii.gz'); epiFile{2} = fullfile('Raw','Ernie_EPI02.nii.gz'); epiFile{3} = fullfile('Raw','Ernie_EPI03.nii.gz'); inplaneFile = fullfile('Raw','ErnieInplane.nii.gz'); anatFile = fullfile('3DAnatomy', 't1.nii.gz');

% Generate the expected generic params structure params = mrInitDefaultParams;

% And insert the required parameters: params.inplane = inplaneFile; params.functionals = epiFile; params.sessionDir = erniePathTemp;

% Specify some optional parameters % 3D volume anatomy (originally from freesurfer) params.vAnatomy = anatFile; % Drop the first 8 volumes in each scan, keep remaining volumes params.keepFrames = [8 -1; 8 -1; 8 -1]; % Subject ID. For most labs, it is probably safest to use an % anonymized coding scheme params.subject = 'Ernie'; % Name for each of the three scans params.annotations = {'PRF 1', 'PRF 2', 'PRF 3'};

% Do the initialization: ok = mrInit(params);

% Open a graphical user interface to ensure that we succeeded vw = mrVista('inplane');

%% Clean up % close(viewGet(vw, 'figure number'); % mrvCleanWorkspace % cd(curdir)

SOURCE END

-->

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