Typical fMRI brain scans take a 3D images of the head every few seconds.  These images are composed of lots of 2D ‘slices’ (usually axially oriented) stacked on top of one another.  This is where the problem of slice acquisition time rears its head – the problem being that these slices are not all taken at the same time, in fact, their collection tends to be distributed uniformly over the duration it takes to gather a whole 3D image.  Therefore, if you are collecting a 3D image comprising 36 slices every 2 seconds, you will have a different slice collected every 1/18th of a second.

2D slices (left; presented as a mosaic), acquired at slightly different times within a 2s TR, that make up a typical 3D image in fMRI (right; shown with a cutout)

If you’re worried about the effect of this fuzziness in temporal resolution on your data (and there are those who don’t), then it can be corrected for in the preprocesisng stages of analysis.  Of course, you do need to know the order in which your slices were collected to correct for the ordering differences.

Finding out the order of slice correction is not as easy as it should be.  On the Siemens Trio scanner that I use, it’s straightforward if you have an ‘ascending’ (bottom to top, in order: 1, 2, 3, etc.) or a ‘descending’ (top to bottom, in order, 36, 35, 34 etc.) order of slice collection.  However, if you’re using the ‘interleaved’ order (odd slices collected first, followed by even slices), it’s not immediately clear whether you’re doing that in an ascending (1, 3 5… 2, 4 6… etc.) or descending (35, 33, 31… 36, 34, 32… etc.) interleaved order.

I found out that I was collecting my slices in an interleaved, ascending order by asking the MR technician at the facility.  But, if there was no technician to hand, or if I wanted to verify this order myself, I would be very tempted to try out a method I found out about on the SPM list today:

Head-turning research (links to poster at a readable resolution on the University of Ghent web-site)

The procedure, devised by Descamps and colleagues, simply involves getting an fMRI participant to turn their head from looking straight up, to looking to one side during a very short scan.  The turn should be caught in its various stages of completion by the various slices that comprise one 3D image, allowing the curious researcher to figure out the slice acquisition order crudely, but effectively.

I enjoyed how connected to the physical reality of our own bodies this procedure is.  It reminded that these tools we are using to make inference about cognition are tied to our bodies in a very tangible way.  That is something I often forget when pushing vast arrays of brain-signals values around in matrices, so it’s nice to be reminded of it now and again – I’d certainly rather be reminded like this, than by having to discard a participant’s data because they have moved so much during the a scan as to make their data useless!

One thought on “The Physical Reality of fMRI Slice Acquisition Order

  1. I know this is an old blog post so I’m not sure what you do now, but you can also get this information by converting the dicoms to nifti using MRICron. Acquisition order information appears in the MRICron terminal at the time of conversion.

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