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Jonathan Winawer edited this page Jul 21, 2016 · 1 revision
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t_alignInplaneToVolume

Illustrates how to align the inplane volume from an fMRI session to the 3D volume anatomy using sample data set erniePRF

Dependencies: Remote Data Toolbox

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

Summary

- Specify alignment matrix linking inplane anatomy to volume anatomy - Save mrSESSION with alignment matrix

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

See also: t_initAnatomyFromFreesurfer t_initVistaSession

Winawer lab (NYU)

Contents

Download ernie raw MRI data 

% Remember where we are
curdir = pwd();

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)

Align inplane to t1 and install Gray/white segmentation 

% NOTE: THIS IS A PLACE HOLDER. WE WILL REPLACE THIS WITH CODE THAT SHOWS
% HOW THE ALIGNMENT IS COMPUTED. FOR NOW WE JUST PROVIDE THE ALIGNMENT
% MATRIX.

% navigate and open vistasession
erniePathTemp = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF');
cd(erniePathTemp)
vw = initHiddenInplane(); % to use the GUI: vw = mrVista;


% aligment matrix (obtained in separate script)
alignMtrx = ...
1.0e+02 * ...
[...
-0.009184260815436  -0.000512038859394   0.007845296072164   2.490305591031722
0.003943260519177  -0.000392116999562   0.018362671991761   1.307013835970514
-0.000316306420987   0.009979180755162   0.001124081482535   0.526943057809918
0                   0                   0   0.010000000000000];


mrSESSION = sessionSet(mrSESSION, 'alignment', alignMtrx);
saveSession();

[niftiCheckQto] NIFTI header origin is at or outside the image volume.
[niftiCheckQto] Origin to the image center [80.000,104.000,12.000] pix.

Visualize 

% open a 3D volume view
vol = open3ViewWindow('volume');

% Define an ROI that is the entire functional slab
vw = newROI(vw, 'inplane', true);
dataSize = viewGet(vw, 'anat size');
[x, y, z] = ind2sub(dataSize, 1:prod(dataSize));
vw = viewSet(vw, 'ROI coords', [x; y; z]);


% Project this ROI to the volume so that we can see the slice selection
% within the volume
vol = ip2volCurROI(vw ,vol);
vol = refreshScreen(vol, 0);

Initializing Volume view
freq_dim not set correctly in NIFTI header.
phase_dim not set correctly in NIFTI header.
[mrLoad]: mr.voxelSize has length<4: concatenating a "1" to it
[mrLoad]: mr.dims has length<4: concatenating a "1" to it
freq_dim not set correctly in NIFTI header.
phase_dim not set correctly in NIFTI header.
Attaching menus
Attaching buttons
Attaching popup menus
Attaching sliders
Done initializing Volume view
Could not find /Users/jonathanwinawer/matlab/git/vistasoft/local/scratch/erniePRF/Volume/userPrefs.mat
freq_dim not set correctly in NIFTI header.
phase_dim not set correctly in NIFTI header.
[mrLoad]: mr.voxelSize has length<4: concatenating a "1" to it
[mrLoad]: mr.dims has length<4: concatenating a "1" to it

Clean up

mrvCleanWorkspace cd(curdir)


Published with MATLAB® R2015a

<!--
SOURCE BEGIN

%% t_alignInplaneToVolume % % Illustrates how to align the inplane volume from an fMRI session to the % 3D volume anatomy using sample data set % % Dependencies: % Remote Data Toolbox % % This tutorial is part of a sequence. Run % t_initAnatomyFromFreesurfer % t_initVistaSession % prior to running this tutorial. % % Summary % % - Specify alignment matrix linking inplane anatomy to volume anatomy % - Save mrSESSION with alignment matrix % % Tested 07/21/2016 - MATLAB r2015a, Mac OS 10.11.6 % % See also: t_initAnatomyFromFreesurfer t_initVistaSession % % Winawer lab (NYU)

%% Download ernie raw MRI data

% Remember where we are curdir = pwd();

%% 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)

%% Align inplane to t1 and install Gray/white segmentation

% NOTE: THIS IS A PLACE HOLDER. WE WILL REPLACE THIS WITH CODE THAT SHOWS % HOW THE ALIGNMENT IS COMPUTED. FOR NOW WE JUST PROVIDE THE ALIGNMENT % MATRIX.

% navigate and open vistasession erniePathTemp = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF'); cd(erniePathTemp) vw = initHiddenInplane(); % to use the GUI: vw = mrVista;

% aligment matrix (obtained in separate script) alignMtrx = ... 1.0e+02 * ... [... -0.009184260815436 -0.000512038859394 0.007845296072164 2.490305591031722 0.003943260519177 -0.000392116999562 0.018362671991761 1.307013835970514 -0.000316306420987 0.009979180755162 0.001124081482535 0.526943057809918 0 0 0 0.010000000000000];

mrSESSION = sessionSet(mrSESSION, 'alignment', alignMtrx); saveSession();

%% Visualize

% open a 3D volume view vol = open3ViewWindow('volume');

% Define an ROI that is the entire functional slab vw = newROI(vw, 'inplane', true); dataSize = viewGet(vw, 'anat size'); [x, y, z] = ind2sub(dataSize, 1:prod(dataSize)); vw = viewSet(vw, 'ROI coords', [x; y; z]);

% Project this ROI to the volume so that we can see the slice selection % within the volume vol = ip2volCurROI(vw ,vol); vol = refreshScreen(vol, 0);

%% Clean up % mrvCleanWorkspace % cd(curdir)

SOURCE END

-->

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