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Jonathan Winawer edited this page Jul 21, 2016 · 5 revisions
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t_initAnatomyFromFreesurfer

Illustrates how to initialize the volume anatomy and class file from a freesurfer directory. Uses the sample freesurfer data set ernie

Dependencies: Freesurfer Remote Data Toolbox

Summary

- Download freesurfer ernie directory - Create t1 anatomy and t1 class files from freesurfer - Visualize the two images

Tested 07/20/2016 - MATLAB r2015a, Mac OS 10.11.6

See also: t_initVistaSession

Winawer lab (NYU)

Contents

Download ernie freesurfer directory 

% Check whether freesurfer paths exist
fssubjectsdir = getenv('SUBJECTS_DIR');
if isempty(fssubjectsdir)
error('Freesurfer paths not found. Cannot proceed.')
end

% Get ernie freesufer1 directory and install it in freesurfer subjects dir
%   If we find the directory, do not bother unzipping again
forceOverwrite = false;


% Do it
dataDir = mrtInstallSampleData('anatomy/freesurfer', 'ernie', ...
fssubjectsdir, forceOverwrite);


fprintf('Freesurfer directory for ernie installed here:\n %s\n', dataDir)

Data directory /Volumes/server/Freesurfer_subjects/ernie already exists. Skipping unzip.
Freesurfer directory for ernie installed here:
/Volumes/server/Freesurfer_subjects/ernie

Create t1 anatomy and t1 class files from freesurfer

Store current directory

curdir = pwd();

%       This is the path where we will set up the vista session
erniePathTemp      = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF');
mkdir(erniePathTemp);


% Navigate
cd(erniePathTemp)


% Create t1 anatomy and class file
mkdir 3DAnatomy;
outfile = fullfile('3DAnatomy', 't1_class.nii.gz');
fillWithCSF = true;
alignTo = 'orig.mgz';
fs_ribbon2itk('ernie', outfile, fillWithCSF, alignTo);


% Check that you created a t1 class file (ribbon) and t1 anatomy
ls 3DAnatomy


% The command window should show:
%       t1.nii.gz	t1_class.nii.gz

Warning: Directory already exists.
Warning: Directory already exists.
mri_convert -rt nearest /Volumes/server/Freesurfer_subjects/ernie/mri/orig.mgz 3DAnatomy/t1.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Volumes/server/Freesurfer_subjects/ernie/mri/orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to 3DAnatomy/t1.nii.gz...
mri_convert --reslice_like 3DAnatomy/t1.nii.gz -rt nearest /Volumes/server/Freesurfer_subjects/ernie/mri/ribbon.mgz 3DAnatomy/t1_class.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Volumes/server/Freesurfer_subjects/ernie/mri/ribbon.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
reading template info from volume 3DAnatomy/t1.nii.gz...
writing to 3DAnatomy/t1_class.nii.gz...



Converting voxels....


Number of L Gray voxels 	= 268982
Number of L White voxels 	= 299585
Number of R White voxels 	= 302175
Number of R Gray voxels 	= 274456
t1.nii.gz	t1_class.nii.gz

Visualize 

% Show the volume anatomy, segmentation, and anatomy masked by segmentation
ni = niftiRead(fullfile('3DAnatomy', 't1.nii.gz'));
t1 = niftiGet(ni, 'data');
ni = niftiRead(fullfile('3DAnatomy', 't1_class.nii.gz'));
cl = niftiGet(ni, 'data');

fH = figure('Color','w');


subplot(1,3,1)
imagesc(t1(:,:,128), [0 255]); colormap gray; axis image
title('Volume anatomy')


subplot(1,3,2)
imagesc(cl(:,:,128), [1 6]);   axis image
title('Class file')


subplot(1,3,3)
mask = cl(:,:,128) > 1;
imagesc(t1(:,:,128) .* uint8(mask));   axis image
title('Masked anatomy')

Clean up 

cd(curdir)


Published with MATLAB® R2015a

<!--
SOURCE BEGIN

%% t_initAnatomyFromFreesurfer % % Illustrates how to initialize the volume anatomy and class file from a % freesurfer directory. Uses the sample freesurfer data set % % Dependencies: % Freesurfer % Remote Data Toolbox % % Summary % % - Download freesurfer ernie directory % - Create t1 anatomy and t1 class files from freesurfer % - Visualize the two images % % Tested 07/20/2016 - MATLAB r2015a, Mac OS 10.11.6 % % See also: t_initVistaSession % % Winawer lab (NYU)

%% Download ernie freesurfer directory

% Check whether freesurfer paths exist fssubjectsdir = getenv('SUBJECTS_DIR'); if isempty(fssubjectsdir) error('Freesurfer paths not found. Cannot proceed.') end

% Get ernie freesufer1 directory and install it in freesurfer subjects dir % If we find the directory, do not bother unzipping again forceOverwrite = false;

% Do it dataDir = mrtInstallSampleData('anatomy/freesurfer', 'ernie', ... fssubjectsdir, forceOverwrite);

fprintf('Freesurfer directory for ernie installed here:\n %s\n', dataDir)

%% Create t1 anatomy and t1 class files from freesurfer % Store current directory curdir = pwd();

% This is the path where we will set up the vista session erniePathTemp = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF'); mkdir(erniePathTemp);

% Navigate cd(erniePathTemp)

% Create t1 anatomy and class file mkdir 3DAnatomy; outfile = fullfile('3DAnatomy', 't1_class.nii.gz'); fillWithCSF = true; alignTo = 'orig.mgz'; fs_ribbon2itk('ernie', outfile, fillWithCSF, alignTo);

% Check that you created a t1 class file (ribbon) and t1 anatomy ls 3DAnatomy

% The command window should show: % t1.nii.gz t1_class.nii.gz

%% Visualize

% Show the volume anatomy, segmentation, and anatomy masked by segmentation ni = niftiRead(fullfile('3DAnatomy', 't1.nii.gz')); t1 = niftiGet(ni, 'data'); ni = niftiRead(fullfile('3DAnatomy', 't1_class.nii.gz')); cl = niftiGet(ni, 'data');

fH = figure('Color','w');

subplot(1,3,1) imagesc(t1(:,:,128), [0 255]); colormap gray; axis image title('Volume anatomy')

subplot(1,3,2) imagesc(cl(:,:,128), [1 6]); axis image title('Class file')

subplot(1,3,3) mask = cl(:,:,128) > 1; imagesc(t1(:,:,128) .* uint8(mask)); axis image title('Masked anatomy')

%% Clean up cd(curdir)

SOURCE END

-->

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