SPM/Information to include in papers

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All papers should give sufficient detail so that if the reader were armed with the authors' data they could reproduce the results (and to a reasonable approximation the actual study). Don't forget to include the version number! Some important items:

Contents

[edit] Image acquisition and preprocessing

  1. Basic image properties: image dimensions and voxel size. Properities of data as acquired *and* after intersubject registration (aka Spatial Normalization). For PET/SPECT, image reconstruction smoothness parameter (e.g. 'ramp filtered', 'Hanning filter, *** mm cutoff').
  2. Was slice timing correction used?
  3. Spatial smoothing. At 1st level and 2nd level if done twice. Kernel type (e.g., Gaussian), kernel width (e.g., 12mm FWHM, note that for a Gaussian kernel it is not enough to write 12mm, since the kernel is infinite).
  4. Basic intrasubject registration info. What software, what sort of interpolation.
  5. Basic intersubject registration parameters. Affine/Linear? If so, how many parameters (9 or 12, typically). If Nonlinear, 'how' nonlinear? (E.g. with AIR, you specify a polynomial order; with SPM, you specify a basis size, like 3x2x3). Regularization setting. What interpolation?
  6. For fMRI, the echo time (TE) should always be reported, since the sensitivity for the BOLD response depends on that.
  7. The selected filtering (especially, the cut-off frequency of the high-pass filter)
  8. To report the order in which the various pre-processing steps have been performed.

[edit] Spaces and spatial normalisation

  1. Template used for normalisation (e.g. "MNI152 T1", "a symmetrical flumazenil template based on 12 controls which was constructed...", "our HMPAO SPECT template as reported in...")
  2. In the description of the results, one should state whether the reported coordinates are MNI or, for example, mni2tal transformed coordinates (and by the use of which tool: Matthew Brett’s, etc.). Or more generally, how the anatomical locations (and/or "Brodmann areas") were determined (e.g. Talairach Daemon, Talairach atlas, etc.).
  3. Regions of Interest: How derived?

test

[edit] Statistics

  1. What voxel-wise statistic image threshold was used? Corrected or uncorrected? FWE or FDR?
  2. Was cluster size inference used? If so, what is the cluster-defining statistic image threshold? What is the cluster size threshold (in voxels) and significance (corrected or uncorrected).
  3. How many voxels corrected for? Whole brain voxel count, or sub-volume count for 'Small Volume Correction'. If small volume correction, define how the sub-region was defined.
  4. If random field theory is used, what is the smoothness (FWHM, x,y,z)? What is the RESEL count? (This allows one to independently recompute the corrected threshold)
  5. to clearly state the threshold used to display results in figures (and make it really explicit when it's different from the one used in the analysis!)
  6. how exactly the contrasts are computed (which condition is subtracted from what, is the contrast masked and if yes by what, etc.). When doing this, use names that explicitely refer to the CONDITIONS/BLOCKS names, not to the names of some underlying variables or psychological concepts (ok, in a perfect and simple world, all should be equivalent, but we don't live in a perfect and simple world, do we?).
  7. The design matricies from the 1st and 2nd levels (use the supplementary information section if necessary). Contrasts could then be specified in terms of design matrix columns (but see the footnote below)
  8. details about the signal converage and SNR in the regions from which results are reported (including regions in which claims are made there are no significant results)
  9. continuous activation maps to be made available - and displayed in the paper or supplementary material. The thresholded maps we are all used to can be seriously misleading (Jernigan TL, Gamst AC, Fennema-Notestine C, Ostergaard AL. More "mapping" in brain mapping: statistical comparison of effects. Hum Brain Mapp. 2003 Jun;19(2):90-5)
  10. it would be very convincing if statistic maps were accompanied by results of an SPMd analysis to demonstrate normal and white residuals (or lack thereof!).

This may sound like a lot, but they are all very basic parameters and can be concisely reported. They also can be reported in detail in one publication from a lab and then cite that publication for details that haven't changed.

[edit] Reporting design matricies

[edit] For

Given that it is readily available from most, if not all fMRI analysis software, the first level and second level design matrices should be included. This could either be in graphical form, or even numerical form. Contrasts could then be specified in terms of design matrix columns. Pretty much all the journals in which we publish allow for online supplementary information, so if these matrices don't fit in the main text, they could be included as supplementary info. In the case that each subject has a slightly different design matrix (i.e. randomised designs or performance-related regressors), a representative 1st level matrix could be included.

[edit] Against

Some of the first-level design matrices can be quite messy (8+ regressors with temporal derivative nuisance variables), and indeed subject dependent if behavioral results are used in analyzing the data. Placing such a graphical representation of these design matrices may be too much information and possibly cumbersome to the reader? Secondly, many 2nd level analyses are either one-sample or two-sample t-tests, which, if graphically represented, would consume precious space (for those page limited journals).

[edit] Other points

  • make a distinction between information that is necessary for other researchers to be able to replicate an experiment, and information not necessarily needed for replication, but that a reviewer might want to see.
  • Please submit your publications to preprint archives online (such as xxx.lanl.gov). Articles can be submitted before -or- after print publication.

[edit] Page contributors

This page is based on SPM JISCMAIL posts by:

  • Thomas Nichols
  • Karsten Specht
  • Mauro Pesenti
  • Tom Johnstone
  • Robert Welsh
  • Alexa Morcom
  • Torben Ellegaard Lund
  • Matthew Brett
  • Daniel Kimberg
  • Max Gunther
  • Jesper Andersson
  • Alexander Hammers
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