Difference between revisions of "FreeSurferToFieldTrip"

From WikiMEG
Jump to: navigation, search
(Created page with "You may think of home improvement as something you would never be able to do at all. Rest assured that there are many easy projects that even a novice can master. This article...")
 
(→‎BEM surfaces: add help functions)
 
(6 intermediate revisions by one user not shown)
Line 1: Line 1:
−
You may think of home improvement as something you would never be able to do at all. Rest assured that there are many easy projects that even a novice can master. This article will help you with home improvement projects that you can master. They will go a long way to improving your home for the future.<br><br>If you must patch small cracks on your roof, using aluminum tape could do the job. Take off the paper backing before applying the tape to a smooth and clean surface. You will now have a waterproof seal to keep out the rain.<br><br>Avoid removing necessary items during construction. Closely examine the area behind cabinet or wall before demolishing it. There could be electrical systems you could damage that would cost quite a bit to fix.<br><br>If your kitchen's counter space is very limited, look into over-the-range microwaves. Installed in place of your stove's range hood, these microwaves come in many different prices and feature configurations. These models use a recirculating filter, making them ideal for use at home or in settings outside professional kitchens.<br><br>Adding texture to your walls with a mix of drywall mud will create an interesting look as well as mask any blemishes. It is quite easy to do. Put the drywall mud on. Use tools to give it texture. A stiff brush will work, as will a sponge, a fork and even a plastic bag. Anything that gives an interesting texture.<br><br>Don't start on your kitchen or bathroom re-do project without first turning off the water supply. As a rule of thumb, if your project involves the water lines, be sure to locate the water shutoff valve to turn the water off before you begin your work. Doing this can help prevent water damage.<br><br>If you want to install a new screen for your window but are unable to find one the right size, it is simple to make one yourself. You can get a kit and attach the screen by using a tool that is fairly cheap. Even if your window requires an external screen with special attachments, you'll find appropriate adapters available that can be easily added to any screen.<br><br>One quick way to change the look of your kitchen is with new knobs and handles on your cabinets. Replacing knobs on cabinets is a easy way to impact the look of your home. When you remove your old knobs and handles, take the opportunity to clean the cabinets inside and out because it's a lot easier without the hardware snagging. Just screw the new knobs onto the doors and your job is complete.<br><br>A house up foe sale needs a good kitchen and bathroom renovation. Bathrooms are more expensive to update than living rooms or bedrooms, and potential buyers can definitely be turned off by having to spend a lot of money updating one. Make sure the sink and tub/shower are in good shape, if not, replace them. Replace linoleum flooring with tile.<br><br>Do not forget that you need to have proper ventalation in your bathroom. Mold takes over when a bathroom retains its moisture. Painting over mold will not totally kill it off. Instead, do something that will prevent it from growing at all. Vents and windows can effectively dehumidify the space.<br><br>There is a ton to know when it comes to home improvement. Don't let it overwhelm you. Your success in a home-improvement process depends on how knowledgeable you are and how much time you are willing to put into it.<br><br>If you beloved this article and also you would like to be given more info about home renovation ([http://www.homeimprovementdaily.com homeimprovementdaily.com]) generously visit our own web-page.
+
The FreeSurfer software provides a good automatic segmentation of T1 images. It includes utilities to generate BEM surfaces that can be used to construct a head model for FieldTrip.
 +
 
 +
The following assumes you've run FreeSurfer on your T1.
 +
 
 +
= Post-recon steps in the shell =
 +
 
 +
Generate BEM surfaces (brain, inner/outer skull & outer skin)
 +
 
 +
<pre>SUBJECTS_DIR=~/mris-tms/fs SUBJECT=anattms_50 mne_watershed_bem</pre>
 +
 
 +
Convert T1 to nifti
 +
 
 +
<pre>mri_convert fs/anattms_50/mri/T1.mgz fs/anattms_50/mri/T1.mgz.nii</pre>
 +
 
 +
Obtain transform from T1 voxels to BEM surface space
 +
 
 +
<pre>mri_info --vox2raw-tkr fs/anattms_50/mri/T1.mgz > fs/anattms_50/transforms/t1-vox2ras-tkr.xfm</pre>
 +
 
 +
= In MATLAB =
 +
 
 +
== Load data ==
 +
Read the Nifti
 +
 
 +
<pre>t1 = ft_read_mri('fs/anattms_50/mri/T1.mgz.nii')</pre>
 +
 
 +
Set the voxel to head space transform, using the file generated previously
 +
 
 +
<pre>t1.transform = load('fs/anattms_50/transforms/t1-vox2ras-tkr.xfm')</pre>
 +
 
 +
Read the BEM surfaces (this function is given below)
 +
 
 +
<pre>bems = read_bem_surfs('fs/', 'anattms_50');</pre>
 +
 
 +
Plot the two together
 +
 
 +
<pre>
 +
ft_determine_coordsys(t1, 'interactive', 'no')
 +
hold on
 +
plot_bem_surfs(bems);
 +
</pre>
 +
 
 +
== To CTF coordinates ==
 +
 
 +
At this point, the T1 and BEM surfaces are in the same coord sys but FieldTrip doesn't know which sys this is, and more importantly, a registration is required with the sensors.  
 +
 
 +
Identify fiducial points (however you like; I use a simple imagesc based function https://gist.github.com/maedoc/97f7d4d4e30c9123e748)
 +
 
 +
<pre>
 +
fids = gofish(t1);
 +
t1 = ft_volumerealign(fids, t1);
 +
</pre>
 +
 
 +
Now, the T1 has a CTF based coord system, but the BEM surfaces need to have their vertices updated (again, this is defined below):
 +
 
 +
<pre>bems = update_bems_coord_sys(bems, t1.transform/t1.transformorig);</pre>
 +
 
 +
Now verify again everything's aligned
 +
 
 +
<pre>
 +
ft_determine_coordsys(t1, 'interactive', 'no')
 +
hold on
 +
plot_bem_surfs(bems);
 +
</pre>
 +
 
 +
== building the FieldTrip head model ==
 +
 
 +
= Helper functions =
 +
 
 +
== BEM surfaces ==
 +
 
 +
<pre>
 +
function bem = read_bem_surfs(subjects_dir, subject)
 +
 
 +
surfs = {'brain', 'inner_skull', 'outer_skull', 'outer_skin'}; %, 'head'};
 +
 
 +
for i=1:length(surfs)
 +
if ~strcmp(surfs{i}, 'head')
 +
bname = [subject '_' surfs{i} '_surface'];
 +
fname = fullfile(subjects_dir, subject, 'bem', 'watershed', bname);
 +
 
 +
% not used for the moment, this is a high resolution surface (~300k vert)
 +
% whereas outer_skin is good enough
 +
else
 +
bname = 'lh.seghead';
 +
fname = fullfile(subjects_dir, subject, 'surf', bname);
 +
end
 +
[v, f] = freesurfer_read_surf(fname);
 +
bem.(surfs{i}).vertices = v;
 +
bem.(surfs{i}).faces = f;
 +
end
 +
 
 +
bem.surfs = surfs;
 +
</pre>
 +
 
 +
<pre>
 +
function ps = plot_bem_surfs(bems)
 +
%
 +
% bems = read_bem_surfs(..)
 +
% ps = plot_bem_surfs(bems);
 +
 
 +
surfs = {'brain', 'inner_skull', 'outer_skull', 'outer_skin'};
 +
colors = {[1 1 1] [1 0 0] [0 1 0] [0 0 1]};
 +
 
 +
for i=1:length(surfs)
 +
si = surfs{i};
 +
p = patch(bems.(si));
 +
set(p, 'edgealpha', 0.0);
 +
set(p, 'facealpha', 0.2);
 +
set(p, 'facecolor', colors{i});
 +
ps.(si) = p;
 +
end
 +
 
 +
axis equal
 +
</pre>
 +
 
 +
<pre>
 +
function bems = update_bems_coord_sys(bems, xfm)
 +
 
 +
surfs = {'brain', 'inner_skull', 'outer_skull', 'outer_skin'};
 +
 
 +
for i=1:length(surfs)
 +
si = surfs{i};
 +
v = bems.(si).vertices;
 +
v = [v ones(size(v, 1), 1)];
 +
v = v*xfm';
 +
bems.(si).vertices = v(:, 1:3);
 +
end
 +
</pre>

Latest revision as of 16:20, 5 May 2015

The FreeSurfer software provides a good automatic segmentation of T1 images. It includes utilities to generate BEM surfaces that can be used to construct a head model for FieldTrip.

The following assumes you've run FreeSurfer on your T1.

Post-recon steps in the shell

Generate BEM surfaces (brain, inner/outer skull & outer skin) 

SUBJECTS_DIR=~/mris-tms/fs SUBJECT=anattms_50 mne_watershed_bem

Convert T1 to nifti 

mri_convert fs/anattms_50/mri/T1.mgz fs/anattms_50/mri/T1.mgz.nii

Obtain transform from T1 voxels to BEM surface space 

mri_info --vox2raw-tkr fs/anattms_50/mri/T1.mgz > fs/anattms_50/transforms/t1-vox2ras-tkr.xfm

In MATLAB

Load data

Read the Nifti 

t1 = ft_read_mri('fs/anattms_50/mri/T1.mgz.nii')

Set the voxel to head space transform, using the file generated previously 

t1.transform = load('fs/anattms_50/transforms/t1-vox2ras-tkr.xfm')

Read the BEM surfaces (this function is given below) 

bems = read_bem_surfs('fs/', 'anattms_50');

Plot the two together 

ft_determine_coordsys(t1, 'interactive', 'no')
hold on
plot_bem_surfs(bems);

To CTF coordinates

At this point, the T1 and BEM surfaces are in the same coord sys but FieldTrip doesn't know which sys this is, and more importantly, a registration is required with the sensors.

Identify fiducial points (however you like; I use a simple imagesc based function https://gist.github.com/maedoc/97f7d4d4e30c9123e748) 

fids = gofish(t1);
t1 = ft_volumerealign(fids, t1);

Now, the T1 has a CTF based coord system, but the BEM surfaces need to have their vertices updated (again, this is defined below): 

bems = update_bems_coord_sys(bems, t1.transform/t1.transformorig);

Now verify again everything's aligned 

ft_determine_coordsys(t1, 'interactive', 'no')
hold on
plot_bem_surfs(bems);

building the FieldTrip head model

Helper functions

BEM surfaces

function bem = read_bem_surfs(subjects_dir, subject)

surfs = {'brain', 'inner_skull', 'outer_skull', 'outer_skin'}; %, 'head'};

for i=1:length(surfs)
	if ~strcmp(surfs{i}, 'head')
		bname = [subject '_' surfs{i} '_surface'];
		fname = fullfile(subjects_dir, subject, 'bem', 'watershed', bname);

	% not used for the moment, this is a high resolution surface (~300k vert)
	% whereas outer_skin is good enough
	else
		bname = 'lh.seghead';
		fname = fullfile(subjects_dir, subject, 'surf', bname);
	end
	[v, f] = freesurfer_read_surf(fname);
	bem.(surfs{i}).vertices = v;
	bem.(surfs{i}).faces = f;
end

bem.surfs = surfs;

function ps = plot_bem_surfs(bems)
%
% bems = read_bem_surfs(..)
% ps = plot_bem_surfs(bems);

surfs = {'brain', 'inner_skull', 'outer_skull', 'outer_skin'};
colors = {[1 1 1] [1 0 0] [0 1 0] [0 0 1]};

for i=1:length(surfs)
	si = surfs{i};
	p = patch(bems.(si));
	set(p, 'edgealpha', 0.0);
	set(p, 'facealpha', 0.2);
	set(p, 'facecolor', colors{i});
	ps.(si) = p;
end

axis equal

function bems = update_bems_coord_sys(bems, xfm)

surfs = {'brain', 'inner_skull', 'outer_skull', 'outer_skin'};

for i=1:length(surfs)
	si = surfs{i};
	v = bems.(si).vertices;
	v = [v ones(size(v, 1), 1)];
	v = v*xfm';
	bems.(si).vertices = v(:, 1:3);
end
Retrieved from "https://meg.univ-amu.fr/index.php?title=FreeSurferToFieldTrip&oldid=24325"