In this practical you will learn to use the main tools for structural analysis: FAST (tissue-type segmentation), FIRST (sub-cortical structure segmentation) and FSL-VBM (local grey matter volume difference analysis). In addition there are several optional extensions, including SIENA, that will be relevant to those with interests in particular types of structural analysis. We advise people to pick and choose based on their own particular interests; everyone should do FAST, but after that the parts are quite separate and can be done in any order (e.g. people particularly interested in VBM might want to do that before the section on FIRST).
In this section we will segment single T1-weighted images with FAST and look at how to quantify the grey matter volume and amount of bias field present.
To begin with we will prepare data for FAST; this requires running BET for brain extraction. In addition, just for this practical, we will also extract a small ROI containing a few central slices so that FAST only takes a minute to process the data, instead of 10-15 minutes for a full brain.
Run BET on the input image
structural to create
Bet for the GUI
Bet_gui on a Mac], or
bet for the command-line
View the output to check that BET has worked OK (e.g. change the colourmap
structural_brain to say Red-Yellow):
fsleyes structural structural_brain &
Back in the terminal, create a cut-down version (containing a few central
slices) of the brain-extracted image using the region-of-interest program
fslroi. This will let you try out some of the FAST options
without having to wait more than a minute each time.
fslroi structural_brain structural_brain_roi 0 175 0 185 100 5
structural_brain_roi into FSLeyes to see the cut-down
image. See how few slices are left. Leave FSLeyes open for the moment.
You will also find an image in this directory called
structural_brain_7T.nii.gz which contains a section of the same
brain acquired on a 7 Tesla scanner with a different bias field or
inhomogeneity, and a cut-down version
structural_brain_7T_roi.nii.gz to the already open FSLeyes
(or open a new one and load
structural_brain_roi first) and then
look at the difference between these images. Note how both grey matter and
white matter are darker in the left anterior portion of the 7T image.
Run FAST (separately) on both
structural_brain_7T_roi. Use the GUI (
Fast_gui on a Mac]) and turn on the Estimated bias field
button (which saves a copy of the bias field) and Restored input button
(which corrects the original image with the calculated bias field). For both
images also open the Advanced Options tab and change the Number of
iterations for bias field removal to 10 to account for the strong bias fields
in both cases.
Finally, don't forget to check that the output name is different for the
two runs (
structural_brain_7T_roi)! Once this is set up
press Go for both - they should only take a minute to run.
Now let's look at the bias field outputs -
structural_brain_7T_roi_bias (these are FAST's estimates of the
bias fields). View these in FSLeyes and set the display ranges to be equal for
both images (e.g. 0.6 to 1.4). Notice how different the two bias fields
Open both of the
*_seg.nii.gz output segmentations in
FSLeyes. Try using different colour maps for the segmentations when viewing
the results. You can now see how a different bias field can alter the
segmentation of the image.
Now let's look at the partial volume segmentations. View the
different outputs in FSLeyes by first loading
structural_brain_roi_restore, then loading the PVE (Partial
Volume Estimate) images as overlays, adjusting the overlay opacity as
necessary. Note that you can tell FSLeyes what colourmaps and intensity ranges
to use from the command line:
fsleyes structural_brain_roi \ structural_brain_roi_pve_0 -cm green -dr 0.5 1 \ structural_brain_roi_pve_1 -cm blue-lightblue -dr 0.5 1 \ structural_brain_roi_pve_2 -cm red-yellow -dr 0.5 1 &
Identify which PVE component is the grey matter. Choose a voxel on the border of the grey matter and look at the values contained in the three PVE components. The values represent the volume fractions for the 3 classes (GM, WM, CSF) and should add up to one. Now pick a point in the middle of the grey matter and look at the three values here.
The PVE images are the most sensitive way to calculate the tissue volume
which is present. For example, we can find the total GM volume
fslstats by doing:
fslstats structural_brain_roi_pve_1 -M -V
The first number reported by
fslstats gives the mean voxel GM
PVE across the whole image, the second is the number of voxels and the third number gives the total volume of the image (in mm3). Multiplying the first and third numbers together will give the total GM volume in mm3 (for more details on fslstats just
fslstats to see its usage description).
In this section we lead you through examples of subcortical structure segmentation with FIRST, and some post-fitting statistical analyses.
We begin by segmenting the left hippocampus and amygdala from a single
T1-weighted image. The image is
con0047_brain.nii.gz. Load this into FSLeyes to start with to see the image. Note that although this is not normally
done, this image has had brain extraction run on it. This is due to the anonymisation done to the original image.
To perform the segmentation of the left hippocampus and amygdala we simply need to run one command:
run_first_all -i con0047_brain -b -s L_Hipp,L_Amyg \ -o con0047 -a con0047_brain_to_std_sub.mat
This command will run several steps for you and has several options. It will take about 4-5 minutes to run, so while it is running read through the following description.
run_first_all script uses the best set of parameters
(number of modes, intensity reference) to run for each structure, as
determined by empirical experiments. Therefore it is not necessary to specify
these values when running the method.
Normally the affine registration would be run as part of this script (just
leave off the
-a option and it will be done automatically), but
it has been pre-supplied here in order to save time - as the registration
takes about 6 minutes.
We will now go through how this script works and what to look for in the output.
Load the image
con0047_brain_to_std_sub.nii.gz together with the
1mm standard space template image into FSLeyes. Look at the alignment
of the subcortical structures. It should be quite close but we do not expect
it to be perfect.
This registration is normally created by
run_first_all as the
initial stage, but has been included here from a previous run to save time.
The registration should always be performed using the tools in FIRST since it
does a special registration, optimised for the sub-cortical structures. It
begins with a typical 12 DOF affine registration using FLIRT, but then refines
this in a second stage with a sub-cortical weighting image that concentrates
purely on the sub-cortical parts of the image. Thus the final registration
may not be as good in the cortex but will better fit the sub-cortical
structures. However, this registration only removes the global affine
component of the differences in the structures and hence will not be that
precise. In addition it, crucially, leaves the relative orientation
(pose) between the structures untouched.
Always make sure you check that the registration has worked before looking at other outputs.
We will now move onto looking at the other outputs which should have been
run_first_all at this point. If the
run_first_all command has not finished have a quick look at
the FIRST documentation page.
Before doing anything else we will check the output logs to see if any errors have occured. Do this with the command:
If everything worked well you will see no output from this, otherwise it will show the errors. If any errors are shown, ask a tutor about them. You should always check the error files in the log directories for FIRST and other FSL commands that create log directories like this (e.g. TBSS, FSL-VBM, BEDPOSTX, etc.).
In FSLeyes, open the image
con0047_brain and add the
con0047_all_fast_firstseg on top.
*_firstseg image shows the combined segmentation of all
structures based on the surface meshes that FIRST has fit to the image. It is
in the native space of the structural image (not in the standard space,
although the registration before was required to move the model from the
standard space back into this image's native space).
As converting the underlying FIRST meshes to a voxel-based image can create
overlap at the boundaries, these boundary voxels have been
"corrected" or re-classified by
run_first_all using the
default method (here it is FAST - which classifies the boundary voxels
according to intensity). Now look at the uncorrected segmentations with the
fsleyes con0047_brain con0047_all_fast_origsegs.nii.gz \ -cm Red-Yellow -dr 0 118 &
Each structure is labeled with a different intensity value inside and 100 +
this value for the boundary voxels (the
con0047_all_fast_origsegs image is a
4D image with each structure in a different volume). The intensity values
assigned to the interior of each structure is given by
Have a look at these images to see how good the segmentation is. Play with the opacity settings (or turn the segmentation on and off) to get a feeling for the quality.
The corrected image (
*_firstseg) is normally the one that you
would use to define an ROI or mask for a particular subcortical structure. For
more details on the uncorrected image (
*_origsegs) -- see
the optional practical at the end.
Vertex analysis (or shape analysis) looks at how a structure may differ in shape between two groups (e.g., patients and controls). It looks at the differences directly in the meshes, on a vertex by vertex basis. This is different from using a whole-structure summary measure like volume, as it allows us to visualise the region of the shape that differs as well as the type of shape difference.
first_utils tests the differences in vertex location - here we
will look at the difference in the mean vertex location between two groups of
subjects, but it can also look for correlations. It projects the vertex
locations onto the normal vectors of the average surface, so that it is
sensitive to changes in the boundary location.
Here we will use an example dataset consisting of 8 subjects (5 controls and 3 Alzheimer's patients) which we will do an analysis on. As the numbers are low it will have fairly low statistical power, but in this case it still shows a clear effect. A full analysis, on a larger set of subjects, would proceed in exactly the same way.
List the files in this directory - we have already run FIRST on each subject in order to get a segmentation of the left hippocampus. So you will see files such as:
con0047_brain.nii.gz con0047_brain_to_std_sub.mat con0047_brain_to_std_sub.nii.gz con0047.com con0047-L_Hipp_corr.nii.gz con0047-L_Hipp_first.bvars con0047-L_Hipp_first.nii.gz con0047-L_Hipp_first.vtk con0047.logs
Most of them should be familiar from the previous example. Because only a
single structure was run, the uncorrected segmentation is saved
con0047-L_Hipp_first and the boundary corrected segmentation
is saved as
con0047-L_Hipp_corr (rather than the names used
before in the case of multiple structures). However, for vertex analysis we
will be using the
.bvars files as they contain the information
about the sub-voxel mesh coordinates.
In general, to run shape analysis, you need to do the following:
-soption). We then use the
.bvarsfiles for the vertex analysis.
Check that the segmentations worked. In order to visualise the
segmentation outputs of FIRST on a large number of subjects it is useful
to generate summary reports that can be assessed efficiently. This can be
easily done using
first_roi_slicesdir, which shows an ROI
(with 10 voxel padding) around the structure of interest for each subject,
summarised into a single webpage. In this case run:
first_roi_slicesdir *brain.nii.gz *L_Hipp_first.nii.gz
and then view the output
index.html in a web browser (it will
be created in a subdirectory called
slicesdir/). Check that
none of the segmentations have failed; make sure that you look at the
axial, coronal and sagittal slices.
Combine all the mode parameters (
.bvars file) into a
single file. Each structure (model) that is fit with FIRST will generate a
.bvars file. For a given structure
(e.g. hippocampus) combine all the relevant
concat_bvars script. Note that the order here is
very important, as it must correspond to the order specified in the design
matrix to be used later for statistical testing. For this example,
.bvars files (all of the left hippocampi) using
concat_bvars all.bvars *L_Hipp*.bvars
which (due to alphabetical ordering) puts the 5 control subjects first, followed by the 3 subjects with the disease.
Create a design matrix. The subject order should match the order in
.bvars were combined in
concat_bvars call. The design matrix is most easily
created using FSL's Glm tool (a single column file). To do
this, start the
Glm GUI (
mac). First, choose the Higher-level/non-timeseries design option from the top pull
down menu in the small window. Next, set the # inputs option to be 8 (the
number of subjects we have in this example).
In the bigger window (of the Glm GUI) set the values of the EV (the numbers in the second column) to be -1 for the first five entries (our five controls) and +1 for the next three entries (our three patients). Leave the group column as all ones. Once you've done this, go to the Contrasts and F-tests tab. The default t-contrast here is fine (there's not much else you can do with a single group difference EV) but we also need to add an F-test. So change the number in the F-tests box to 1, and then highlight the button on the right hand side (under F1) to select an F-test that operates on the single t-contrast.This F-test will be the main contrast of interest for our vertex analysis as it allows us to test for differences in either direction.
When this is all set up correctly, save everything using
the Save button in the smaller Glm window. Choose the current
directory and use the name
design_con1_dis2 (as we will
assume this is the name used below, although for your own studies you can
use any name of your choice). Now exit the Glm GUI.
We are now ready to run
first_utils and perform the vertex
We will do the analysis using
--useReconMNI to reconstruct the
surfaces in MNI152 space (though note that an alternative would be to
reconstruct the surfaces in the native space
Perform the first part of vertex analysis using the command:
first_utils --usebvars --vertexAnalysis -i all.bvars \ -o diff_con1_dis2_L_Hipp_mni -d design_con1_dis2.mat --useReconMNI
first_utilscommand on a personal install of FSL, it may fail unless FSL is installed at
first_utils command uses the combined bvars input,
created above with
concat_bvars, and the design
design_con1_dis2.mat. The other options specify that this
command is to prepare an output for vertex analysis (since it can also do
other things) in standard space (
first_utils has run you are now ready to carry out the
cross-subject statistics. We will use
randomise for this, as the
FIRST segmentations are unlikely to have nice, indepedent Gaussian errors in
them. Normally it is recommended to run at least 5000 permutations (to end up
with accurate p-values), but with a small set of subjects like this there is a
limit to how many unique permutations are available, so in this analysis all unique permutations will be run.
For multiple-comparison correction there are several options available
in randomise and we will use the cluster-based one here (
although other options may be better alternatives in many cases. The call to
randomise (using the outputs from
first_utils, which includes
a mask defining the boundary of the appropriate structure, as well as
the design matrix and contrasts formed above) is:
randomise -i diff_con1_dis2_L_Hipp_mni.nii.gz \ -m diff_con1_dis2_L_Hipp_mni_mask.nii.gz \ -o con1_dis2_L_Hipp_rand -d design_con1_dis2.mat \ -t design_con1_dis2.con -f design_con1_dis2.fts \ --fonly -D -F 3
The most useful output of
randomise is a corrected p-value
image, where the values are stored as 1-p (so that the interesting, small
p-values appear "bright"). The corrected p-value file is the one
corrp in the name. This correction is the
multiple-comparison correction, and it is only this output which is
statistically valid for imaging data - uncorrected p-values should not be
reported in general, although they can be useful to look at to get a feeling
for what is in your data. The statistically significant results are therefore
the ones with values greater than 0.95 (p<0.05), and in this case the file is
To view the data in FSLeyes, on top of the standard brain, do the following:
fsleyes -std1mm \ con1_dis2_L_Hipp_rand_clustere_corrp_fstat1 -cm red-yellow -dr 0.95 1 &
Note that this specifies the display range (0.95 to 1.0) and a useful colourmap (Red-Yellow) in order to easily see the results.
Find the hippocampus in this image and look to see where the significant differences in shape have been found using this vertex analysis. Normally we would not expect to find much in a group of 8 subjects, but these were quite severe AD cases and so the differences are very marked.
.bvarsfiles output by FIRST and a design matrix. These contain all the information required by
--useReconMNI, use the
first_utilswill align each surface to the mean shape (from the model used by FIRST) with 6 degrees of freedom (translation and rotation). The transformation is calculated such that the sum-of-squared distances between the corresponding vertices is minimized. This command is needed when using
--useReconNative, however, can be used with
--useReconMNIto remove local rigid body differences.
--useScaleflag can be used in combination with
--useRigidAlignto align the surfaces using 7 degrees of freedom.
--useScalewill indicate to
first_utilsto remove global scaling.
In this section we look at a small study comparing patients and controls for local differences in grey matter volume, using FSL-VBM. Most of the steps have already been carried out, as there isn't enough time in this practical to run all of the registrations required to carry out a full analysis from scratch.
ls in the directory. Note that we have
renamed the image files with some prefixes so that all controls and patients
would be organised in "blocks". This is to make the statistical
design easily match the alphabetical order of the image files (who will be
later concatenated to be statistically analysed).
We have 10 controls and 8 patients and wish to carry out a
control>patient comparison. First, we need to define the statistical
design, which here will be a simple two-tailed t-test to compare both
groups. For this, use the
Glm GUI to generate
design.con files, using the
Higher-level/non-timeseries design option in the GLM setup window.
At this point, you need to enter the appropriate overall number of subjects as
inputs in the GLM setup window (here n=18, then press enter), and then use the
Wizard button of the GLM setup window with the two groups, unpaired
option and appropriate number of subjects for the first group (here
ncontrols=10). If the design looks correct, then save it by
pressing Save in the GLM setup window and give it the output basename
design. In this analysis, only the
design.con files will be used.
Moreover, as we have more controls than patients, you will need to list the
subjects used for the creation of the study-specific template by missing out
the last 2 controls for instance (
con_4098.nii.gz), so that the number of controls used to
build this study-specific template matches the number of patients in
template_list text file (we have provided this for you here). The contents of this file should therefore
look like this:
con_1623.nii.gz con_2304.nii.gz con_2878.nii.gz con_3456.nii.gz con_3641.nii.gz con_3642.nii.gz con_3668.nii.gz con_3670.nii.gz pat_1433.nii.gz pat_1650.nii.gz pat_1767.nii.gz pat_2042.nii.gz pat_2280.nii.gz pat_2632.nii.gz pat_2662.nii.gz pat_2996.nii.gz
Check the contents of this
template_list file by doing:
We first ran the initial FSL-VBM script:
This moved all the original files into the
origdata folder; to
see what they all look like, run this command to view
slicesdir report in a web browser:
firefox origdata/slicesdir/index.html &
fslvbm_1_bet command has also created some brain-extracted
images. We actually ran
fslvbm_1_bet both with the
-b option and then, because the original
images have a lot of neck in them, which was often being left in by the
default brain extractions, we ran using the
-N option. Compare
the different results from the two options by loading in the two web
firefox struc/slicesdir-b/index.html & firefox struc/slicesdir-N/index.html &
It should be very obvious which option is working well and which one isn't!
Next, all the brain images are segmented into the different tissue types, and then the study-specific GM template is created, by registering all GM segmentations to standard space, and averaging them together. The command used was:
You can view all of the alignments to the MNI152 initial standard space by running the following, and turning on FSLeyes movie mode ():
fsleyes struc/template_4D_GM &
and then view the alignment of the study-specific template to the MNI152 standard space with:
fsleyes -std struc/template_GM -cm blue-lightblue -dr 0.2 1 &
Finally, the registrations to the new, study-specific, template
were run for all subjects, and modulated by the warp field expansion
(Jacobian), before being combined across subjects into the 4D image
stats/GM_mod_merg. An initial GLM model-fit is run in order to
allow you to view the raw tstat images at a range of potential smoothings.
This was achieved by running (don't run this!):
So now you can have a look at the initial raw tstat images created at the different smoothing levels, pick the one you "like" best. You can change the colour maps for each tstat in FSLeyes to more clearly see the differences.
cd stats fsleyes template_GM -dr .1 1 \ GM_mod_merg_s4_tstat1 -dr 2.3 6 \ GM_mod_merg_s3_tstat1 -dr 2.3 6 \ GM_mod_merg_s2_tstat1 -dr 2.3 6 &
The different images that you can see in the
GM_mod_merg_s2 / 3 / 4
GM_mod_merg_s2_tstat1 / s3 / s4
design.mat / design.con
You are now ready to carry out the cross-subject statistics. We will
randomise for this, as the above steps are very unlikely to
generate nice Gaussian distributions in the data. Normally we would run at
least 5000 permutations (to end up with accurate p-values), but this takes a
few hours to run, so we will limit the number to 100 (to get a quick-and-dirty
result). We will also use TFCE thresholding (Threshold-Free Cluster
Enhancement - this is explained in the randomise lecture) which is similar to
cluster-based thresholding but generally more robust and sensitive.
For example, if you decide that the appropriate amount of smoothing is with
a sigma of 3mm, then the following will run
randomise with TFCE and a reduced number of 100 iterations:
randomise -i GM_mod_merg_s3 -o tmp -m GM_mask \ -d design.mat -t design.con -n 100 -T
Once randomise has finished look at the results (corrected for multiple comparisons) in FSLeyes:
fsleyes template_GM -dr .1 1 \ tmp_tfce_corrp_tstat1 -cm red-yellow -dr 0.8 1 &
In this example we set the corrected p-threshold to 0.2 (i.e. 0.8 in FSLeyes), because of the reduced number of subjects in this example and hence low sensitivity to effect - you would not be able to get away with this in practice!
SIENA is a package for both single-time-point ("cross-sectional") and two-time-point ("longitudinal") analysis of brain change, in particular, the estimation of atrophy (volumetric loss of brain tissue).
cd ~/fsl_course_data/seg_struc/siena ls
The example data is two time points, 24 months apart, from a subject with probable Alzheimer's disease. The command that was used to create the example analysis is (don't run this - it takes too long!):
siena sub3m0 sub3m24 -d -m -b -30
-d flag tells the siena script not to clean up the many
intermediate images it creates - you would not normally use this. The other
options are explained later.
SIENA has already been run for you. Change directory into the SIENA output directory:
cd sub3m0_to_sub3m24_siena ls
In the SIENA output directory the first timepoint image is named
"A" and the second "B", to keep filenames simple and
short. To view the output report, open
report.html in a web
browser. The next few sections take you through the different parts of the
webpage report, which correspond to the different stages of the SIENA
First BET was run on the two input images, with options telling it to create the skull surface image and the binary mask image, as well as the default brain image.
Other BET options can be included in the call to siena by adding
-B "betopts" - for example
siena sub3m0 sub3m24 -d -m -b -30 -B "-f 0.3"
the command line tells
siena to pass on the
option to BET, which causes the estimated brain to be larger if the value used
is less than 0.5, and smaller otherwise.
You also might need to use the
-c option to BET if you need to
tell BET where to center the initial brain surface, such as when you have a
huge amount of neck in the image. For example, if it looks like the centre of
the brain is at 112,110,78 (in voxels, e.g. as viewed in FSLeyes),
and you want to combine this option with the above
-f option, you
would add, to the siena command,
siena sub3m0 sub3m24 -d -m -b -30 -B "-f 0.3 -c 112 110 78"
You can see the two brain and skull extractions in the webpage report. If you want to see these in more detail, open the relevant images in FSLeyes, for example:
fsleyes A A_brain -cm red-yellow A_brain_skull -cm green &
Be aware that the skull estimate is usually very noisy but that it is only used to determine the overall scaling and this process is not very sensitive to the noise as long as the majority of points lie on the skull.
Now the two time points are registered using the script
siena_flirt. This runs the 3-step registration (brains, then
skulls, then brains again). The transformation is "halved" so that
each image can be transformed into the space halfway between the two. The
webpage report shows the alignment of the two brains in this halfway
space. You need to check that the two timepoints are fundamentally
well-aligned, with only small (e.g. atrophy) changes between them. Look out
for mistakes such as: the two images coming from different subjects, one image
being left-right flipped relative to the other one, or one image having bad
If you want to look at the registration in more detail:
fsleyes A_halfwayto_B_brain B_halfwayto_A_brain &
Now, if standard-space-based masking has been requested (it was in
this case, using the -m option in the command above), the two brain images are registered to the standard brain
$FSLDIR/data/standard/MNI152_T1_2mm_brain using FLIRT. The
transforms (and their inverses) are saved. The two brains are registered
separately and their transforms compared to test for consistency.
The webpage report shows the two images transformed into standard space, with the overlaying red lines derived from the edges of the standard space template, for comparison.
-m option was set, a standard space brain mask is now
transformed into the native image space and applied to the original brain
masks produced by BET. This is in most areas a fairly liberal (dilated) brain
mask, except around the eyes.
-b options are set then an upper or
lower limit (in the Z direction) in standard space is defined, to supplement
the masking. This is useful, for example, to restrict the field-of-view of the
analysis if you have variable field-of-view at the top or bottom of the head
in different subjects.
The webpage report shows the
-m brain masking in blue,
-b masking in red (you can see the effect of
-b -30 option), and the intersection of the two maskings in
green. It is this intersection that is what gets finally used.
In order to find all brain/non-brain edge points, tissue-type segmentation is now run on both brain-extracted images. The GM and WM voxels are combined into a single mask, and the mask edges (including internal ventricle edges) are used to find edge motion (discussed below). The webpage report shows the two segmentations.
The final step is to carry out change analysis on the registered masked brain images. At all points which are reported as boundaries between brain and non-brain, the distance that the brain surface has moved between the two time points is estimated. The mean perpendicular surface motion is computed and converted to PBVC (percentage brain volume change).
The webpage report shows the edge motion colour coded at the brain edge points, and then shows the final global PBVC value. To see the edge motion image in more detail:
fsleyes A_halfwayto_B_render -cm render1 &
We now look at 4 examples of "problem cases" - these were real cases that occurred in one study; they illustrate some of the problems/mistakes that sometimes occur.
report.html in a web browser.
Look at the FLIRT A-to-B registration results. Can you tell what's wrong? If you're unsure, click here.
The subject IDs have gotten mixed up - the two timepoint images are from different subjects! (Also, BET is including too much neck, but that's not the main problem....)
report.html in a web browser.
Look at the FLIRT A-to-B registration results. Can you tell what's wrong? If you're unsure, click here.
One of the datasets has been left-right flipped (look at the axial slices in the registration animation), despite one of them having been marked with a right-side marker at some point...(and, yes, again BET is not working well on this data).
report.html in a web browser.
Look at the FLIRT A-to-B registration results. Can you tell what's wrong? If you're unsure, click here.
Both original images have some movement artefact (ringing) and are quite noisy. It's probably not worth keeping data of this quality. Look in the coronal slices in the registration animation. Also, something else is odd....the images are clearly identical - they must have originally been the SAME timepoint by mistake. The slight boundary differences must be due to slightly different BET results caused by only one of the images having the right-side marker (seen in the top BET result image).
report.html in a web browser.
The second dataset has bad motion artefact, and one of the datasets has been left-right flipped...
In this section we look at how SIENAX works and look at the most useful outputs. SIENAX estimates total brain tissue volume, from a single image, normalised for skull size.
report.html in a web browser. The example data is one
time point from a subject with probable Alzheimer's disease. The command that
was used to create the example analysis is (don't run this!):
sienax sub3m0 -d -b -30 -r
SIENAX starts by running BET and FLIRT in a manner very similar to SIENA, except that the second time point image is replaced by standard space brain and skull images. Next a standard space brain mask is always used to supplement the BET segmentation.
As before, optional Z limits in standard space can be used to mask further.
Next, FAST is used, with partial volume estimation turned on, to provide an accurate estimate of grey and white matter volumes. In order to provide normalised volumes for GM/WM/total, the volumetric scaling factor derived from the registration to standard space is used to multiply the native volumes; the values are thus normalised for head size.
Interesting output images are (view with FSLeyes):
overlayprogram, to make the overlay appear more transparent, for clarity.)
Because we used the
-r option, we also have two extra regional
measurements. Use FSLeyes to view
I_vent_render; here the CSF PVE
image has been masked by a standard-space (dilated) ventricle mask, to enable
SIENAX to estimate ventricular CSF (the colouring is a little hard to see as
it was rendered transparently). Now view
I_periph_render; here the GM PVE image has been masked by a
standard-space cortex mask to try to remove cerebellum, brain stem, ventricles
and deep grey - it's not perfect but it's not bad....
This follows on from the initial part of the FIRST practical above and
run_first_all has been successfully run. Having
considered the boundary corrected segmentation previously, we now turn to look
at the uncorrected segmentation.
The uncorrected segmentation shows two types of voxels: ones that the underlying surface mesh passes through (boundary voxels) and ones that are completely inside the surface mesh (interior voxels). FIRST uses a mesh to model the structure when doing the segmentation, so converting this to a volume requires it to be split into boundary and interior regions like this.
We will now look at the uncorrected volumetric segmentations:
fsleyes con0047_brain con0047_all_fast_origsegs &
To view the segmentation better change the colourmap of the segmented image to Red-Yellow and make the Max display range value to 100 for this image. Note that you see the interior voxels and the boundary voxels in different colours. This is because the boundary voxels are labeled with a value equal to 100 plus that of the interior voxels. That is, the interior and boundary voxels for the left hippocampus are labeled 17 (the CMA label designation for left hippocampus) and 117 respectively.
con0047_all_fast_origsegs is a 4D file containing
each structure's segmentation in a separate 3D file. If you change
the Volume control on FSLeyes to go from 0 to 1 then you will see the
left amygdala result. These are separated in case these uncorrected
segmentations overlap. Play with the opacity settings (or turn the
segmentation on and off) to see how good the segmentation is.
These images require boundary correction which is done automatically
run_first_all. However, there are alternative methods for
doing the boundary correction which you can specify
run_first_all or as a post-processing on the uncorrected
first_boundary_corr, although the settings used
run_first_all have been chosen as the optimal ones based on
Multi-channel segmentation is useful for when the contrast or quality of a single image is insufficient to give a good segmentation. Typically, this type of segmentation is not needed for healthy controls with good T1-weighted images, as the single channel results are good and are often even better than the multi channel results. However, when pathological tissues/lesions are present, or when the T1-weighted image quality is not good, multi-channel segmentation can take advantage of the extra contrast between tissue types in the different images and give better results.
sub2_t2 are T1-weighted and
T2-weighted images of the same subject. Are they well aligned? You can get an
easy non-interactive combined view of two images (which must have the same
image dimensions) with
slices sub2_t1 sub2_t2
They look reasonably aligned in sagittal and coronal view, but axial views
clearly show misalignment between scans (if you cannot clearly see the axial slices, open the same two images in FSLeyes). Before running multi-channel FAST it
is necessary to use FLIRT to register the data. Start by running
Bet on each
image to remove the non-brain structures, producing
sub2_t2_brain. Note that it is
OK if one of the brain extraction results includes non-brain matter
(e.g. eyeballs) but the other is accurate, since the brain mask used by FAST
will be the intersection of the two masks.
Start the FLIRT GUI:
For this example use the following settings:
sub2_t1_brain(clear the existing directory name in the file browser and press enter to get to the local directory).
sub2_t2_to_t1 into FSLeyes
to check the result of the registration. Change the colour map for the higher
image in the list to Red-Yellow and increase its transparency so that
you can see how good the overlap is.
You can now forget
Fast (with the Number of input
channels set to 2) on the multi-channel brain-extracted
sub2_t2_to_t1_brain (or whatever you called these BET
outputs). Asking for the default number of classes (3 - assumed to be
GM/WM/CSF) gives poor results because bits of other tissues outside of
the brain are given a class - so you should run with 4 classes; then
results should be good. This takes a few minutes; move on to the next
part of the practical and view the results once
fast has finished
If you have time to spare after finishing the other practical parts then you can come back and test the effect of various FAST options, obtained by typing:
You could also work out how to colour-overlay segmentation results
onto the input image using the