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Hi Michael, Thanks u for your quick response ! My dMRI scans were angled (the ang. AP, RL & FH are not zero) - so is this means I need to use the rotated bvecs instead of gradient table that comes out from the DICOM header ? Is it true to say that it is always necessary to use the rotated table (or just always use it and in cases were the dMRI scans were acquired in a strictly transverse plane, the rotatation just won't matter and the 2 tables will be the same ? Thanks for your help !!! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel 2014-07-20 19:03 GMT+03:00 Harms, Michael <[log in to unmask]>: > > Were your dMRI scans acquired in a strictly transverse plane (relative > to the gradient axes), or were they angled in some fashion? If the latter, > it is possible that MRIconvert is rotating the bvecs into the space of the > dMRI scans, which is what FSL expects. The converter 'dcm2nii' definitely > does this (if used with default options), so you could compare the bvecs > from MRIconvert against those returned by 'dcm2nii'. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [log in to unmask] > > From: Rotem Saar <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Sunday, July 20, 2014 5:28 AM > To: FSL - FMRIB's Software Library <[log in to unmask]> > Subject: [FSL] Diffusion analysis - difference between gradients tables > > Dear FSL experts, > > I'm currently trying to analyze Diffusion data in FSL. I'm working with > dicoms from a 3T Philips scanner, 33 directions*60 slices, Bvalue = 800. > I used MRIconvert and transformed the dicoms into FSL-NIFTI format. It > created all the necessary files. > At the first step, I'm interested in extracting the FA & MD maps. > The thing is - when I look at the gradient matrix created using MATLAB > script that reads the directions from the dicom header - I get one table, > but the bvecs file created in MRIconvert looks different. > So my question is which table should I use for diffusion analysis in FSL? > The one that was created from the dicom header or the one created for > FSL-NIFTI format ? Do u have any idea as to why is there a difference ? > > I will really appreciate your help, > > Thanks ! > > Rotem Saar-Ashkenazy > > Department of Brain and Cognitive Science > Ben Gurion University of the Negev, Beer-Sheva, 84105 > > School of Social Work > Ashkelon Academic College, Ashkelon, 78211 > > Israel > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. >