TechnicalNoteReferenceSlice - MRC CBU Imaging Wiki

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WHat wOrd is made by the captiaL lettErs?

location: TechnicalNoteReferenceSlice

Lauri has discovered a potential pitfall for those of you using slice-timing correction on data from the Trio (using standard sequences).

1. Our standard sequences acquire the slices from top to bottom (ie descending). Thus the correct slice order for slice-timing correction is [N:-1:1], where N is your number of slices (eg 32) and the slice number refers to the position of the slice within the image file and in our case 1=last slice acquired (eg bottom slice). This is normally the done correctly.

2. However, if you have specified the reference slice to be slice 1 (as is default in AA, for example), you WILL need to change the default reference timebin used in your subsequent 1st-level statistical analysis (to be the last timebin, eg 16, to match the fact that the data are synchronised to the last slice acquired). Otherwise your model will be 1 TR shifted with respect to your data, which can cause problems the longer the TR and the shorter your SOA (generally speaking).

In other words, if you done Step 1 above and not explicitly changed the reference slice, you will need to change the reference timebin for your stats. This is called the "microtime onset" when you use the GUI, which should be equated to the "microtime resolution" (which is 16 by default). Or if you use batch scripts, you need to set:

  • SPM.xBF.T0 = SPM.xBF.T (assuming SPM.xBF.T already set to, eg, 16).

Alternatively, you can change the reference slice during slice-time correction to the first slice acquired (eg "top" slice, ie N here), either via the GUI when you run slice-timing, or if you use AA, by:

  • aap.spmanalysis.sliceorder = [32:-1:1]; aap.spmanalysis.refslice = 32;

Do one or t'other, not both!*


* Except for those of you who have asked me directly about this issue, when I usually recommend changing BOTH the reference slice to the mid-slice-acquired and the reference timebin to the mid-timebin.

Dr Richard Henson MRC Cognition & Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF, UK

Tel: +44 (0)1223 355 294 x522 Fax: +44 (0)1223 359 062