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Hi Mark, Thanks for the prompt replay! Could you please share some of tips on checking the outputs? Thank you! Frank On Tue, Aug 7, 2012 at 2:38 PM, Mark Jenkinson <[log in to unmask]> wrote: > Hi, > > As far as I am aware there is nothing specific in the script that is > targeted at any particular type of Siemens scanner but it has not been > tested on all scanner types and all scanner software versions, so please do > check the outputs carefully. > > All the best, > Mark > > > > On 7 Aug 2012, at 22:05, Liang-Tien Hsieh wrote: > > Hi Mark, Just wanted to double check, would the script also work for > Siemens skyra scanners? > > Thank you! > Frank > > On Tue, Aug 7, 2012 at 6:21 AM, Mark Jenkinson <[log in to unmask]>wrote: > >> Hi, >> >> This script doesn't actually mention Verio, it mentions Varian, which is >> a type of scanner we used to have in our lab in Oxford. The Varian code is >> not useful to anyone outside Oxford and isn't even mentioned in the usage. >> >> The script should be fine for all current Siemens scanners - as far as I >> know - but make sure you check the outputs to make sure. >> >> All the best, >> Mark >> >> >> >> On 7 Aug 2012, at 14:14, Geranmayeh, Fatemeh wrote: >> >> > Dear Mark >> > >> > Can you please confirm if this script is safe to use with Siemens Trio. >> > The script text mentions Siemens Verion. >> > >> > Many thanks >> > >> > Fatemeh >> > >> > >> > >> > Dr Fatemeh Geranmayeh >> > Wellcome Trust Clinical Research Fellow >> > The Computational, Cognitive and Clinical Neuroimaging Laboratory >> > Imperial College London >> > Telephone : 020 7594 7994 >> > >> > >> > >> > >> > >> > On 24/07/2012 18:04, "Mark Jenkinson" <[log in to unmask]> wrote: >> > >> >> Hi, >> >> >> >> This is going to be in our upcoming release, but in the meantime you >> can >> >> find a copy of fsl_prepare_fieldmap at: >> >> http://www.fmrib.ox.ac.uk/fsldownloads/patches/ >> >> >> >> This just needs to be copied to $FSLDIR/bin/ on your machine. >> >> Note that this is only designed to work with Siemens data at present. >> >> >> >> All the best, >> >> Mark >> >> >> >> >> >> On 24 Jul 2012, at 13:57, Fatemeh Geranmayeh wrote: >> >> >> >>> Dear Experts. >> >>> >> >>> I am following the instructions given at 2012 FSL course on how to >> >>> process fieldmap phase difference images acquired by Siemens. ( Page >> 286 >> >>> of the handout). The command fsl_prepare_fieldmap does not work, >> and I >> >>> can not get the usage command by just typing it either. I note someone >> >>> else raised this issue back in May. I have tried both >> >>> fsl_prepare_fieldmap, and prepare_fieldmap command. There are no >> manual >> >>> /help entry for this. >> >>> >> >>> >> >>> Can you help? >> >>> >> >>> Best wishes >> >>> Fatemeh >> >>> >> > >> > > >