Maintaining acquisition and analysis data quality

It is important that those running FMRI experiments feed back relevant information to Rhodri Cusack (physics), the radiographers (many issues), the ImagersInterestGroup, the CBU methods group (many analysis and acquisition methods issues) and RhodriCusack (aa analysis in SPM). Anything that will further understanding of the best way to acquire and analyse data is appreciated. If you have a problem, please be constructive, and don't complain when your MR study has failed just because we don't yet fully understand the brain. There will be meetings to discuss data quality every few months open to all using the scanner, as part of the IIG series.If you are designing an experiment, here are some issues you may wish to consider, and a default recommendation for each option.

<<TableOfContents: execution failed [list index out of range] (see also the log)>>

Slice order

Brief description

The scanner may acquire slices in an interleaved spatial order (e.g., where 1= bottom slice, 2= next slice up and so on, slices 1, 3, 5... n-1, 2, 4, 6...n) or sequentially, moving always in one direction throughout the acquisition. Both of these may be done in an ascending or descending direction.

Advantages of interleaved over sequential

Advantages of sequential over interleaved

Ascending vs. descending

There is a possibility that if an ascending acquisition is used, the blood flowing up into the brain will be repeatedly excited and saturated. We do not know the degree of this effect.

The default recommendation has changed (3/4/2006): We now suggest that you use a sequential descending sequence (rather than interleaved ascending) unless you plan to reduce the distance factor, ie gap between slices.

Prospective movement correction

Brief description

In contrast to the usual type of FMRI movement correction, which is done offline as part of the preprocessing procedure, the scanner may also perform prospective movement correction (P A C E), in which the scanner measures the position of the head from an EPI acquisition, and then changes the angle and position of the slices to be acquired. The reconstruction (fourier transform from k-space to provide brain images) and movement measurement are done as fast as possible and slice changes are applied to the acquisition that starts 1 TR after the end of the one used to determine the parameters (i.e., lag of 2 TRs).

Possible advantages

Possible disadvantages

This default has changed (3/4/2006). If you are doing real-time analysis, switch on the prospective correction. If you are not, we recommend that do not use it unless you have a reason to think it is particularly appropriate for your study. Further evaluation is to be performed soon.

Distance factor

Brief description

There is a gap between slices, determined by the "distance factor" which is the size of the gap specified as a proportion of a slice.

Advantages and disadvantages

The default distance factor is 25%, with 3 mm slices, giving a gap of 3mmx0.25=0.75mm, and a slice-to-slice distance of 3.75 mm.

Repetition time (TR), field of view & resolution

Brief description

There is a tradeoff between resolution and TR

Advantages and disadvantages

How many slices?

The default of 32 slices will cover most of the brain in most subjects. However, if you are also interested in the cerebellum, 36 slices is recommended (this results in a 2.19 second TR). If potentially missing even a few mm of inferior cerebellum (while also acquiring motor cortex) in your biggest-headed subject is a problem, 38 slices may be necessary. Also see note about increasing field of view below.

The default CBU sequence has a TR=2s, with 32 slices of 64x64 matrix size, giving a 192x120mm field of view with a resolution of 3x3x3.75 mm. We usually use a slice angle of around 30 degrees to avoid the eyeballs. Typical coverage is shown below on two sample brains.

Note that the person on the left has an unusually large head, and you might want to increase the field of view a little in the ant-post direction , as there will be "wrap around" in your EPIs in this direction, in which the bit of scalp just outside the field of view on the front will appear on the back of your images, and vice-versa.


Slice thickness & angle

Brief description

Because voxels are anisotropic, and different encoding directions are differentially sensitive to field inhomogeneities, the angle of slices can affect the signal loss in regions where there is dropout. The slice thickness also has an effect, as smaller voxels have less of a field change across them for a given field gradient.

Choosing these parameters

Rik Henson collected the following data to investigate the effect of slice thickness and angle in the frontal lobes. The angles specify the pitch, with positive values corresponding to the slices tipping down towards the front.


A summary of the effects: 1. Less drop-out for thinner slices (compare middle left with middle right panel) - but worse coverage of course

2. Less lateral posterior temporal drop-out when tilting up at front (eg compare top right with middle right panel)

3. ...but more anterior temporal drop-out when tilting up at front (compare where cursor is for top left versus middle left panel)

Note that: i) all volumes contain 32 slices, TR=2.120, each re-shimmed to FoV.

ii) tilts are expressed relative to approximate AC-PC line, which was 12 degrees


Brief description

Two coils are available - a 12 channel head coil and a single channel transmit/receive coil.

Advantages and disadvantages

The 12 channel coil.

Segment vs. normalise

Brief description

SPM 5 included a new method of performing normalisation, which is simultaneous grey/white segmentation and normalisation.

Advantages and disadvantages

Written by RhodriCusack Apr 2006 following meeting on Apr 3. Thanks to all those present for their input.