I take your point that the review process should be such that papers
that are insufficiently clear with respect to the experimental design
should be caught. But often I think this is not the case, partly because
of the lack of standard guidelines about what level of detail is
necessary, and partly because I think that a non-negligible number of
reviewers aren't familiar enough with the maths to realise the potential
sensitivity of fMRI analyses to seemingly minor details (such as the use
or not of derivatives at the 1st level, or the extent of colinearity). I
think that the provision of space for online supplemental material can
take care of this without impacting on limited journal space.
Tom
----- Original Message -----
From: Robert Welsh <[log in to unmask]>
Date: Tuesday, February 15, 2005 9:06 am
Subject: Re: [SPM] Any Papers on Presenting fMRI Results?
> I know from our own studies some of the first-level design matrices
> canbe quite messy (8+ regressors with temporal derivative nuiscance
> variables), and indeed subject dependent if behavioral results are
> usedin analyzing the data. Placing such a graphical representation
> of these
> design matrices may be too much informtation 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).
>
> In a certain way, shouldn't the peer review process just bear
> weight on
> this issue? The text of any paper should read such that the analysis
> methodology is well understood, and of course needs to provide for a
> clear picture of how the data give rise to published results. I
> stronglysupport the concept that data are well presented in a
> succinct and
> cogent manner in any paper, but surely alot of the responsibility lies
> on the shoulder of the reviewer and the editorial staff of any peer
> review journal. Those papers pass the muster of of review process but
> then subsquently have done a piss-poor-job with its prose and
> descriptions of the scientific methods employed will suffer in the
> citation column. "A paper Darwinism" (which I dread perverting
> Darwin'sname for the sake of a catch-phrase. My apologies)
>
> My two cents
>
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> Robert C. Welsh, PhD
> Research Investigator
> Department of Radiology
> University of Michigan
> (734) - 764 - 2412 (fax)
> [log in to unmask]
>
>
> >>> IAIN T JOHNSTONE <[log in to unmask]> 02/15/05 9:37 AM
> >>>
> Given that it is readily available from most, if not all fMRI analysis
> software, I would suggest that the first level and second level design
> matrices are 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
> representative1st level matrix could be included.
>
> Another thing that I think should be included (perhaps also as
> supplementary info) is details about the signal converage and SNR in
> the regions from which results are reported (including regions in
> whichclaims are made there are no significant results). Lack of
> adequate SNR
> might explain many of the discrepant results across different
> labs/experiments.
>
> I would be very happy to be part of a working group looking into
> formulating some standard recommendations. This would tap nicely into
> the project comparing different fMRI analysis software packages
> that I
> am currently engaged in.
>
> Tom Johnstone
> Waisman Lab for Brain Imaging and Behavior
> University of Wisconsin-Madison
>
> ----- Original Message -----
> From: Jesper Andersson <[log in to unmask]>
> Date: Tuesday, February 15, 2005 3:46 am
> Subject: Re: [SPM] Any Papers on Presenting fMRI Results?
>
> > Hi guys,
> >
> > just wanted to add a related comment.
> >
> > People are increasingly starting to take more than one parameter
> > estimate per subject to the second level (e.g. HRF+derivatives).
> > In this
> > case the sensitivity/specificity of the results will depend
> > crucially on
> > the outcome of the estimation of the variance components, but at the
> > present time there isn't really any readily avilable information
> that> can be used to report in a paper.
> >
> > I am guessing that the weights of "covariance-matrix-basis-
> functions"> are slightly to esoteric for most people (certainly is
> for me).
> >
> > So, Karl/Will would it be possible to calculate also the
> corresponding> Greenhouse-Geiser correction factor, not for actual
> use on the
> > data, but
> > for giving an intuitively interpretable number that can be used for
> > reporting?
> >
> > Puss Jesper
> >
> >
> > > 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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