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That was indeed the one I was thinking about, but I have never tried this option, and I am sorry to se it fail. Best Torben > Den 27. jun. 2016 kl. 11.12 skrev Leonardo Tozzi <[log in to unmask]>: > > Dear Torben, > > > Thank you very much for your swift and thorough reply. > Sadly, the dataset has been already acquired and passed to me for analysis. Therefore, I would be especially interested in how to correct for these effects post-acquisition if possible. > When you talk about Jacobian modulation, do you mean using the "Realign and Unwarp" dialog and setting the Jacobian deformations option to Yes? If I do that and leave the other settings as default, the unwarping fails and I get the following error: > > > Unwarp terminated abnormally. > Failed 'Realign & Unwarp' > Error using size > Too many output arguments. > In file "/Users/tozzil/Documents/MATLAB/Apps/spm12/spm_uw_estimate.m" (v6456), function "uwAtA2" at line 630. > In file "/Users/tozzil/Documents/MATLAB/Apps/spm12/spm_uw_estimate.m" (v6456), function "build_AtA" at line 580. > In file "/Users/tozzil/Documents/MATLAB/Apps/spm12/spm_uw_estimate.m" (v6456), function "spm_uw_estimate" at line 353. > In file "/Users/tozzil/Documents/MATLAB/Apps/spm12/config/spm_run_realignunwarp.m" (v6554), function "spm_run_realignunwarp" at line 90. > > The following modules did not run: > Failed: Realign & Unwarp > > Are there any settings that should be manually changed for this procedure? > Thank you very much, > > > > Leonardo Tozzi, MD > > PhD Student > > Trinity College Institute of Neuroscience > > College Green, Dublin 2 > > Ireland > From: Torben Lund <[log in to unmask]> > Sent: Monday, June 27, 2016 10:42:50 AM > To: Leonardo Tozzi > Cc: [log in to unmask] > Subject: Re: [SPM] Hyperintensity artefact close to edge of field of view > > Dear Leonardo > > It looks like signal pile-up near air tissue interfaces due to B0 inhomogenieties. You can reduce this at the acquisition stage by using in-plane acceleration e.g. GRAPPA, smaller voxels or different angulation of the slices. Modulation with the jacobian during unwrap might reduce this. > > Best > Torben > > > Sendt fra min iPhone > > Den 27. jun. 2016 kl. 08.43 skrev Leonardo Tozzi <[log in to unmask]>: > >> Dear experts, >> >> I am currently working on a task fMRI dataset (TR: 2s, TE: 35ms, voxel size: 3x3 mm2, 4.8 mm slice thickness, 550 dynamic scans, 23 slices per volume). >> While preprocessing the data on SPM, I noticed that it shows a hyperintensity in the anterior cingulate cortex and inferior temporal lobes, close to the edge of the field of view. This looks like an artefact to me: it seems to be common across subjects (see screenshot 1: 5 subjects after warping at volume 1) and within the time series of each subject (see screenshot 2, one subject volumes 100:108). >> I was wondering if someone had any suggestions on how to correct this artefact (if possible) and, otherwise, some insight on how it might impact the analysis of task related activity using a GLM. In particular, I am concerned it might affect the detection of task effects in the subgenual portion of the ACC, especially after smoothing. >> >> Thank you for your help. >> Yours faithfully, >> >> >> Leonardo Tozzi, M.D. >> >> PhD Candidate >> Discipline of Psychiatry >> Trinity College Institute of Neuroscience >> College Green >> Dublin 2 >> Ireland >> >> Office: +35318964234 >> Mobile: +353851026166 >> <1.png><2.png>