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Hi, Tim, I know all you said because I am an MRI physicist to run my scanner. All I want to know is FSL rule to write a correct input file bvecs. My question is very simple but your answers are not direct and clear. Let me put my question more clearly: I know G_read, G_x and they are not the same for my case. Is x_1 in the bvecs I am going to write should be the G_read or G_x? Li -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Tim Behrens Sent: 26 June 2007 11:35 To: [log in to unmask] Subject: Re: [FSL] bvecs If G_read is the gradient along the read orientation, (i.e. the x direction of your image) then this is what you have to use. If you acquire in pure axial then presumably G_read=G_x if G_read is something else, and you don't acquire in pure axial, then you have to rotate your scanner frame coordinates (G_x?) to match the rotation of your image acquisition from pure axial. T On 26 Jun 2007, at 11:16, Li Sun wrote: > Hi, Stephen, > I understand that the bvecs need to be relative to the image space. My > question is how do you set up your rule for your software which is not > clear in your original document: should x_1 be the first value of > G_read > or G_x of the diffusion weighting gradient direction vector? > Li > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf Of Steve Smith > Sent: 26 June 2007 09:19 > To: [log in to unmask] > Subject: Re: [FSL] bvecs > > > Hi - the bvecs need to be relative to the image space - otherwise they > don't mean anything to the processing software! Cheers. > > > > On 25 Jun 2007, at 15:32, Li Sun wrote: > >> HI, >> From FSL document, bvecs contains x_1 ..., it seems gradient >> directions in the real world, ie, Gx, Gy and Gz but I am not sure if >> it is true. If >> it is, as what I got from my scanner is DWG-read, DWG-phase and >> DWG-slice, I can find out and convert them to corresponding >> orientations >> in the real world. For example, G-read is -Gx, G-phase is -Gz, and >> G-slice is +Gy, and how do I deal with negtive, ie, -Gx and -Gz? >> Is it >> also related to display the results with FSLView? >> Li > > > ---------------------------------------------------------------------- > -- > > --- > Stephen M. Smith, Professor of Biomedical Engineering Associate > Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > ---------------------------------------------------------------------- > -- > > ---