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Beg pardon, I'm new to this field, I assume that when you say "supplementary web information" you do not mean the entirety of the article _plus additional information_ available online. One way around journal restrictions is always to post your articles (plus all relevant information for duplication of results), to xxx.lanl.gov's neuroscience page. Lena p.s. I'm used to doing research using xxx.lanl.gov, and I have considerably better access to it than to paper journals. -----Original Message----- From: SPM (Statistical Parametric Mapping) on behalf of Alexa Morcom Sent: Wed 2/16/2005 9:37 AM To: [log in to unmask] Cc: Subject: Re: [SPM] Any Papers on Presenting fMRI Results? In principle, standardisation and agreement has to be a good thing - I guess time will tell when the field is 'ripe' for it... For now, I'll add my couple of thoughts - Do we need to give more detail than, for example, papers based on behavioural or ERP data? It's not usually considered necessary to include residual plots in these cases. Do we want to make imaging papers intelligible to non-expert-imagers and to non-imagers? I think this is important, and so would want to avoid too much technical detail in papers - such as design matrices, which in any case are software-specific - just enough to enable replication and to make it clear that the important issues have been dealt with appropriately. I don't know about supplementary web-based information - it's nice, but I imagine that not everyone has easy access to it - and one can always contact the authors. If it's really important, shouldn't it be in the paper? If anyone's interested, something like this was done for ERPs by Picton et al (2000, Psychophysiology. 2000 Mar;37(2):127-52) Alexa -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On Behalf Of Torben Ellegaard Lund Sent: 16 February 2005 01:17 To: [log in to unmask] Subject: Re: [SPM] Any Papers on Presenting fMRI Results? Interesting discussion this one I guess Tom will be too polite to mention this. But I think 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!). Unfortunately for first level analysis it is really only an option for the SPM folks. But I think SPMd would serve as a great quality check. best torben Torben E. Lund Danish Research Centre for MR Copenhagen University Hospital Kettegaard Allé€ 30 2650 Hvidovre Denmark email: [log in to unmask] webpage: http://www.drcmr.dk On 16 Feb 2005, at 01:35, Matthew Brett wrote: 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.