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Dear Michelle Occasionally putting a mean interpolated image is necessary. If a participant moved their head outside the acquisition volume (say they moved 5cm) then this would otherwise zero all voxels in the mask from the run so you end up not getting whole brain coverage. You should still put the null regressor(s) in for each bad volume. Or exclude the participant if you can afford it. Also see http://www.ncbi.nlm.nih.gov/pubmed/23861343 Best wishes, Simon > -----Original Message----- > From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] > On Behalf Of Carmichael, David > Sent: 04 November 2015 16:40 > To: [log in to unmask] > Subject: Re: [SPM] Artrepair and Motion Regressors > > Dear Michelle, > > You should really include a regressor for those that you have catagorised as > 'bad', or you have altered your effective degrees of freedom in you data > without properly accounting for it. However this extra regressor makes the > interpolation pointless because the effect of the regressor is to remove the > variance associated with that volume. > > You will find the approach of adding regressors to account for large motion > events in a GLM described in the following paper. > Modelling large motion events in fMRI studies of patients with epilepsy. > Lemieux L, Salek-Haddadi A, Lund TE, Laufs H, Carmichael D. > Magn Reson Imaging. 2007 Jul;25(6):894-901. > http://www.ncbi.nlm.nih.gov/pubmed/17490845 > > You can also find a very effective alternative/addition to art repair > FIACH: A biophysical model for automatic retrospective noise control in > fMRI. > Tierney TM, Weiss-Croft LJ, Centeno M, Shamshiri EA, Perani S, Baldeweg T, > Clark CA, Carmichael DW. > Neuroimage. 2015 Sep 28; > http://www.ncbi.nlm.nih.gov/pubmed/26416652 > > You can download the tools here > http://www.homepages.ucl.ac.uk/~ucjttie/index.html > > Best regards > David > David Carmichael > Reader in Neuroimaging and Biophysics > Honorary Reader, Radiology, Great Ormond Street Hospital NHS Foundation > Trust > > Developmental Imaging and Biophysics Section Developmental > Neurosciences Program UCL Institute of Child Health > 30 Guilford Street > London, UK > WC1N 1EH > > Tel +44 (0) 2079052298 > Fax +44 (0) 2079052358 > > http://www.action.org.uk/our_research/epilepsy_improving_brain_scanning > _surgery > > https://iris.ucl.ac.uk/research/personal/index?upi=DWCAR66 > > > -----Original Message----- > From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] > On Behalf Of Achterberg, M. > Sent: 04 November 2015 09:02 > To: [log in to unmask] > Subject: [SPM] FW: Artrepair and Motion Regressors > > > > -----Original Message----- > From: Achterberg, M. > Sent: woensdag 4 november 2015 10:02 > To: 'H. Nebl' > Subject: RE: Artrepair and Motion Regressors > > Dear Helmut, > > Thank you for your advice! > What we've now done is the second option, so replacing bad volumes by > interpolated good ones. > Would you then recommend including one regressor with all repaired > volumes in it, or a separate regressor for each repaired volume? > > Thanks in advance! > > Best, Michelle > > -----Original Message----- > From: H. Nebl [mailto:[log in to unmask]] > Sent: dinsdag 3 november 2015 14:27 > To: [log in to unmask]; Achterberg, M. > Subject: Re: Artrepair and Motion Regressors > > Dear Michelle, > > I'd say you have to provide some more details on the Artrepair features you > want to use for your preprocessing, as it provides several options: A very > simple strategy (which I personally prefer due to its simplicity) would be to > just calculate the scan-to-scan motion, then go on with the default > preprocessing and add dummy regressors to the design matrices for each of > the bad volumes (possibly also for the preceding and the successive volumes) > when setting up the models, in addition to the rp file. This way you would > model each of the bad volumes separately. As normalisation and smoothing > might reduce global signal artefacts it might be better to rely on the > realigned files in that case. > > However, you can also replace bad volumes by interpolated good ones. You > would usually still want to deweight them from analysis though, as it's > artificial data, and you would still add the rp files (as you "controlled" for the > volumes with fast head motion but not for the slow changes over time). This > might be somewhat problematic though, as the rp files might still include > jerks that are no longer present in the data (because the volumes were > replaced by other data, resulting in a smoother transition). > > Then, there's also the "Motion Adjustment" feature (see > http://cibsr.stanford.edu/content/dam/sm/cibsr/documents/tools/methods > /artrepair-software/MotionandDespike.pdf ), which is meant as a > replacement for adding rp files. The proposed preprocessing pipeline is > described in the manual. > > Best > > Helmut