30/5/24, 11:24 How to classify ICA components | Caroline Nettekoven
How to classify ICA components
Caroline Nettekoven
Last updated on Jan 19, 2024 · 10 min read
About this guide
This post explains how to classify noise and signal components obtained from single-subject ICA.
These hand-labelled components can be later used for ICA-based cleaning of fMRI data. I focus here
on the practical steps rather than the theoretical background. For a deeper dive into the methods
and the tools used here, check out the resources linked at the end. For ICA-based noise removal,
have a look at this post.
Background
Classifying components
How do I recognize noise and signal components?
Higher quality datasets
Signal
Noise
Lower quality datasets
Signal
Noise
Features to use for classification
Saving classified component lists
Links and Resouces
Background
In resting-state fMRI processing, we often apply Independent Component Analysis (ICA) to split the
data into components, either to clean the data of structured noise or to analyse the signal compo-
nents we find. In either case, we need to identify which components are noise-driven and which are
dominated by signal.
ICA is a dimensionality reduction method, similar to Principal Component Analysis
(PCA). That means, ICA reduces the high-dimensional raw functional data into a low-
dimensional representation. Put differently, ICA finds patterns in the data that are in-
dependent form each other and explain substantial variance in the data. By breaking
down the data into these patterns, or components, ICA separates the data into com-
ponents that reflect BOLD signal and components that reflect noise (physiological,
imaging reconstruction artefacts, movement, etc.).
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ICA components consist of a single 3D spatial maps and an associated time course. Using the map,
the timecourse and a frequency domain representation of the timecourse, we can identify the noise
components, label them, and regress their associated variance out of the raw data - thereby remov-
ing the noise.
Classifying components
How do I recognize noise and signal components?
In order to separate noise from signal, we need to look at the spatial map, timecourse and power
spectrum and judge whether this reflects more signal or more noise. In general, we don’t want to
throw away any signal, so when in doubt we leave components in the data by labelling the compo-
nents as Unknown. Innoncent until proven guilty is the mantra.
The best way to learn how to recognize noise components in your own data is to look at them. Pull
up the melodic_IC.nii.gz file of an example subject from your dataset and click through the
components.
fsleyes --scene melodic -ad subject-01/run-01.feat/filtered_func_data.ica
I also like to open the plots of the motion parameters generated automatically by the FEAT report.
FEAT only generates these if you have run motion correction within FEAT. For that, run open sub-
ject-01/run-01.feat/report_prestats.html or point your browser at the report_prestats.html
file. This is very useful to compare the timecourse of the component you are looking at with the mo-
tion parameters. Sometimes you can spot a movement noise component by their exact match with
one of the motion parameter timecourses.
If you have not run motion correction within FEAT, but, say, with SPM, you can generate those plots
quickly with fsl_tsplot. The SPM-output text file starting with rp_ contains the movement parameters
of the scan as estimated during SPM motion correction. The file contains six columns. These repre-
sent position (not movement) of the subject in terms of X, Y, and Z displacement and X, Y, and Z axis
rotation with respect to the first scan entered. The first three columns are in millimeters and the last
three are in degrees. Run the following to generate and open the motion parameter plots:
fsl_tsplot -i subject-01/run-01.feat/rp_run_01.txt -t 'SPM estimated rotations (radians)' -u 1 --start=1
fsl_tsplot -i subject-01/run-01.feat/rp_run_01.txt -t 'SPM estimated translations (mm)' -u 1 --start=4 --
fsl_tsplot -i subject-01/run-01.feat/rp_run_01.txt -t 'SPM estimated rotations and translations (mm)' -u
open subject-01/run-01.feat/*_01.png
This should pull up plots like this where you can see the movements (in this case translations in
mm) over time:
By comparing the timecourse of the components for this scan with the movement parameters over
time, you can identify noise components that are dominated by movement.
Higher quality datasets
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In some datasets, noise and signal will be easier to recognize than in others. In high quality datasets,
labelling is usually easier than in datasets of lower quality. Nevertheless, noise shares some features
that are recognizable in dataset of all kinds. I will walk through some examples here, starting with
high quality data to get a feel for what clearly distinguishable noise and signal looks like. The resting-
state scans in this dataset consist of many timepoints (~600 volumes), have a low TR (1 second)
and a relatively small voxel size (2.5 x 2.5 x 3 mm).
Signal
Look at the component below. The spatial map of the component shows signal stemming mostly
form voxels within the brain, that look like they are confined to grey matter (little contribution from
white matter and ventricular voxels). It also looks like biologically plausible signal, since it appears
spatially contiguous. Examine the time series plot in the bottom left corner and the Power spectrum
in the bottom right corner shown in fsleyes. The component is easily identifiable as signal from its
smooth, BOLD-like timecourse (bottom left) that has most of its power at low frequencies below 0.1
Hz (bottom right). Generally, BOLD signal will have its highest power between 0.01 and 0.1 Hz, al-
though higher frequencies can occur.
The same goes for the second signal component. Signal is coming primarily from grey matter vox-
els, that seems biologically plausible, as it appears uninterrupted in several axial slices and contigu-
ous lines that follow a gyral pattern. The timecourse looks smooth and the power spectrum shows
high power in the lower frequency range below 0.1 Hz.
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Noise
Now let’s look at a few noise components. These will usually appear as the earliest components in
the data, so they will explain the most variance. It often can take 10-20 components of noise until
the first signal component pops up, so don’t be surprised if you have to click through quite a few
noise components until hitting some signal! In fact, more than 70% of components will be noise, so
don’t worry if most of what you can find will be noise. The data can still have a lot of signal in it, the
noise components simply outnumber it. But this goes to show how important thorough is for resting-
state data.
Below you can see a clear noise component. The strongest contributions to this component are
made by voxels that are clearly outside of the brain and the timecourse shows sharp jumps. This
component likely comes from a sudden head movement at around volume 490.
Another noise component in the figure below shows very high frequency fluctuations as seen in the
power spectrum and the time series plot. The spatial map shows a ringing around the brain that
does not seem confined to gyri inside the brain.
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Lower quality datasets
The data in the next dataset we will look at is of relatively lower quality, with fewer volumes acquired
(only 100), slightly larger voxels (3 x 3 x 3 mm) and from a patient population that is prone to moving
in the scanner. Still, we can still distinguish some of the noise and signal components clearly in the
data.
Signal
This signal component shows high activity in the grey matter and little to no contributions from vox-
els outside the brain or in white matter and ventricles Although the smoothness of the timecourse is
less pronounced in this signal components because fewer volumes were acquired in this data, it still
shows the low frequency fluctuations we would expect from BOLD signal. The power spectrum
peaks at around 0.1 Hz, as expected.
Spatial map, slow timecourse and the low frequency power spectrum identify this component as sig-
nal as well.
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This component also shows the characteristic contributions from voxels in grey matter that are spa-
tially contiguous, show a smooth timecourse and a low power spectrum of BOLD signal.
Noise
Here, we can see the spatial map clearly indicates noise by the brightest voxels located outside of
the brain in areas that suffer from signal dropout. This noise is likely induced by susceptibility arte-
facts. Due to the few volumes, the timecourse appears less characteristically noisy than we saw in
the noise components of the high quality dataset. Nonetheless, the spatial map is a clear sign that
this component is dominated by noise.
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The typical ringing around the front of the brain identifies this component as noise. Moreover, the
high contributions from voxels within the ventricles and the jumps in the timecourse confirm that
this component should be classified as noise.
The below timecourse shows some signs of noise, but could also contain some signal. Because nei-
ther the spatial map, nor timeseries plot and power spectrum can definitively identify this compo-
nent as noise or signal, this component is left unclassified.
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Features to use for classification
Different spatial and temporal features can hint at components being noise-driven or signal-driven.
The tables below give a summary of features that appear in the spatial map of the components.
These features are also some of the features calculated by FIX for classifier training - in total FIX cal-
culates ~180 features per component. I have covered using FIX to train a classifier for automated la-
belling and data cleaning in a separate blog post. Head over there to learn more about how to use
your hand-labeled training set with FIX.
Spatial feature Signal characteristic Noise characteristic
Clusters’ size and spatial distribution Low number of large clusters High number of small clusters
Voxels overlaying bright/dark raw data voxels More overlap with GM intensity Overlap with e.g. blood vessels
Overlap with brain boundary Low overlap High overlap
Overlap with different tissue types Overlap with GM Overlap with WM, CSF, vessels
Features that appear in the time series plot and the power spectrum of the component are in the ta-
ble below.
Temporal feature Signal characteristic Noise characteristic
Jump (i.e. sudden changes) amplitudes in the time series Fairly smooth time series Large jump
Time series distribution Fairly normal Bimodal or long-tailed
Distribution of power in frequency domain (Fourier transform) Low frequency High frequency
Saving classified component lists
When going through your components in the fsleyes melodic view, make sure to save your labels by
clicking on the Save labels tab and giving it a name like hand_labels_noise.txt (required by FIX). If
you want to train the FIX classifier with these labels, then the format with which fsleyes saves these
files is ideal (info on the format requirements). You should label each component in each of the
scans you are using to train FIX as either Signal or Noise or leave it as Unknown.
To loop quickly through a subset of scans for classification, I usually use this script:
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data_dir=/path/to/your/data/resting_state/imaging_data/
design_dir=~/code/preprocessing/
subjects=(`ls -d ${data_dir}/s??`)
# ------ Classify single-subject ICA components ------
for i in $subjects; do
subject=${i##*s}
# test if subject is in ${design_dir}/classified_subjects.tsv
if grep -q s${subject} ${design_dir}/classified_subjects.tsv; then
run=`grep s${subject} ${design_dir}/classified_subjects.tsv | awk '{print $2}'`
if [ -d $i/run${run}.feat/filtered_func_data.ica ] && [ ! -f $i/run${run}.feat/filtered_func_data
echo CLassifying $i ${run}
# Open motion parameter plots either from report_prestats.html or generate them from rp_r
if [ -f $i/rp_run_${run}.txt ] && [ ! -f $i/rot_${run}.png ]; then
fsl_tsplot -i $i/rp_run_${run}.txt -t 'SPM estimated rotations (radians)' -u 1 --star
fsl_tsplot -i $i/rp_run_${run}.txt -t 'SPM estimated translations (mm)' -u 1 --start=
fsl_tsplot -i $i/rp_run_${run}.txt -t 'SPM estimated rotations and translations (mm)'
fi
if [ -f $i/rot_trans_${run}.png ]; then
open $i/*_${run}.png
else
open $i/run${run}.feat/report_prestats.html
fi
fsleyes --scene melodic -ad $i/run${run}.feat/filtered_func_data.ica
else
echo "Already classified $i ${run}"
fi
else
echo "Not classifying $i"
fi
done
Links and Resouces
I picked up a lot that is covered here from excellent colleagues, including, but not limited to Ludo,
Alberto, and the FSL Course Team. A special mention goes to Ludo’s fantastic teaching materials
and papers on noise classification, which I have linked below:
Paper on Classifying Components: “ICA-based artefact removal and accelerated fMRI acquisition
for improved resting state network imaging”
Educational course slides: “The Art and Pitfalls of fMRI Preprocessing”
FIX Classifier User Guide: Link
FEAT User Guide: Link
Resting-state fmri Task-based fmri Neuroimaging BOLD data MRI analysis Tutorials Teaching
FSL SPM Posts
Related
How to clean fMRI data with FIX-ICA
How to set up FIX on your system
How to inspect surface data
How to fieldmap correct
How to explore functional data
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