Hi,
I would put in a plea for 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
In my experience, continuous maps also give a much clearer picture of
the quality of the data.
Also, it seems to me that any ROIs used should be made available online.
Best,
Matthew
On Mon, 14 Feb 2005 17:36:23 -0500, Thomas E Nichols <[log in to unmask]> wrote:
> Max,
>
> > Is anyone aware of papers about presenting results for fMRI studies?
> > Specifically I'm looking for any attempts that have been made to
> > standardize what is reported and how.
>
> I don't know of any such efforts, but I think it's badly needed. I
> was once asked by an editor for such standards and started to make a
> list of statistical and non-statistical issues. I'd love to hear
> comments on such guidlines.
>
> -Tom
>
> -- Thomas Nichols -------------------- Department of Biostatistics
> http://www.sph.umich.edu/~nichols University of Michigan
> [log in to unmask] 1420 Washington Heights
> -------------------------------------- Ann Arbor, MI 48109-2029
>
> All papers should give sufficient detail so that if the reader were
> armed with the authors' data they could reproduce the results. Some
> important items:
>
> 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 independly
> recompute the corrected threshold)
>
> Not directly related to the statistics, but crucial for any complete
> reporting are:
>
> a. 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').
>
> b. Was slice timeing correction used?
>
> c. Smoothing applied. At 1st level and 2nd level if done twice.
>
> d. Basic intrasubject registration info. What software, what sort of
> interpolation.
>
> e. Basic itersubject registration parmaeters. 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?
>
> 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.
>
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