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Hi When I check the data, I find the system may be unstable in some cases. It randomly occurs in some of my dataset. Best Paul 2015-09-14 18:21 GMT+08:00 Andreas Bartsch <[log in to unmask]>: > Hi, > > it would seem a bit strange to me if RF bias field only affects 10 out of > 500 cases. > Were these scanned with a different coil? > Cheers, > Andreas > > Von: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > Mark Jenkinson <[log in to unmask]> > Antworten an: FSL - FMRIB's Software Library <[log in to unmask]> > Datum: Montag, 14. September 2015 09:27 > An: <[log in to unmask]> > Betreff: Re: [FSL] Artefacts in fMRI data > > Hi, > > It probably won't make a lot of difference in cases where you don't have > much artefact, but you need to test that in order to know for sure. If you > try it on some cases of minimal artefact and see if there is much > difference then that will let you decide whether it is worthwhile applying > it to all 500 or just the ones where it will make a difference (e.g. 10 or > so worst cases). > > All the best, > Mark > > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > KUN HSIEN CHOU <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Saturday, 12 September 2015 11:04 > To: "[log in to unmask]" <[log in to unmask]> > Subject: Re: [FSL] Artefacts in fMRI data > > Hi Mark > > If some of our dataset have this problem [around 10 cases / 500 (whole > dataset)], do we need to perform the same correction approach for the rest > of the dataset or just use this approach to affected data ? > > Best > > Paul > > 2015-09-11 16:19 GMT+08:00 Mark Jenkinson <[log in to unmask]>: > >> Hi, >> >> The example you show is definitely RF bias field (or B1 inhomogeneity) >> and not related to B0 inhomogeneity or distortion. If the temporal SNR in >> the darker regions is still good then this type of artefact doesn't have a >> strong impact on the voxelwise analysis. However, it can affect the motion >> correction and the registration. To remove it (assuming you do not have >> any RF, or B1, mapping scans) then you can calculate the bias field from a >> T1-weighted structural image using FAST and then apply this bias field (if >> you output the bias field from FAST then just multiply this with your >> images) *after* transforming the bias field into the correct space. If >> your fMRI and structural images were acquired in the same session then >> using FLIRT with the -applyxfm and -usesqform (but not -init) options will >> allow you to transform from one space (the structural space, where you've >> calculated the bias field) to the functional space. You can tell if this >> works by just looking at the output after the transformation and >> multiplication and seeing if the image looks more uniform. Do this first, >> prior to any motion correction, and then it will hopefully eliminate all >> problems associated with the bias field. >> >> As for the little shop of horrors - this isn't online anymore, as it is >> out of date. You are better off looking at the papers about FIX: >> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX >> as these papers show a selection of common artefacts in modern data. >> >> All the best, >> Mark >> >> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of >> Sam Rogers <[log in to unmask]> >> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >> Date: Friday, 4 September 2015 11:33 >> To: "[log in to unmask]" <[log in to unmask]> >> Subject: [FSL] Artefacts in fMRI data >> >> Hello. >> >> The MELODIC FAQ ( http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC/FAQ ) >> mentions a fMRI little shop of horror, but the link is broken. I have found >> other resources, but I am not totally sure on this. >> >> I have got some 2x2x2 functional data collected on a 3T scanner where >> some lateral and posterior areas are much brighter. I guess this is bias >> field. I've put an example on the web >> http://postimg.org/gallery/g7q24w9q/ >> >> I have field map data, so I can correct for distortion in B0, but I think >> this is RF related right? What would you suggest best done to resolve this? >> Would you be concerned with the image quality? >> >> Thanks for helping. >> Sam >> >> >