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I think your bvals and bvecs are not in the same order. How did you generate them? Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stamatios Sotiropoulos Sent: Monday, December 20, 2010 7:03 AM To: [log in to unmask] Subject: Re: [FSL] bvecs and bvals are not accepted Hi, On 20 Dec 2010, at 12:42, Mri lab wrote: > Hello, > > First, as we open the dti-data, some of the gradient directions that we have (30) are not seen completely (most of them are working). The placement of the missing data varies between the gradient directions. What could be the problem? > Are you talking about opening the data file with FSLview? In that case you need to be aware that the contrast and brightness settings are set automatically according to the intensities of your first volume, which is a b=0 as far as I can see. The diffusion-weighted volumes have much smaller intensities and will be displayed as really dark images under these settings. If you reduce the max entry (at the top bar of FSLview), you will be able to display these images better. > Second, we wish to obtain DTI-maps by using FDT, however our bvecs and bvals are not accepted. Perhaps something wrong with the text editing? The data is presented here below, where we have 5b0 and 30dir. > What do you mean not accepted? You get an error message? What does it say? If FDT complaints about not finding the bvecs and bvals make sure that your files have the correct names. > bvals: > > 0.329137 0.329137 0.329137 0.329137 0.329137 1500.329137 1500.329137 > 1501.295098 1498.003209 1497.585377 1503.717237 1504.100943 1501.072814 > 1504.006563 1505.230816 1497.527742 1500.793796 1492.638593 1508.782710 > 1494.619833 1502.228976 1504.937093 1500.910644 1494.609534 1488.908011 > 1503.720588 1491.185291 1506.909606 1503.324193 1500.088855 1505.904591 > 1493.632906 1506.647836 1494.364400 1500.149359 > > bvecs: > > 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000000 0.166021000 -0.109967000 0.901242000 -0.169023000 -0.814711000 0.656035000 0.582241000 0.900189000 0.693299000 0.356853000 0.543141000 -0.525144000 -0.639216000 -0.329966000 -0.524029000 0.60876000 0.220055000 -0.003999000 -0.510701000 0.413837000 -0.678931000 0.883949000 0.261995000 0.087982000 0.293958000 0.887045000 0.256977000 0.085993000 0.863255000 > 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000000 0.986122000 0.663802000 -0.419113000 -0.601083000 -0.385863000 0.36602000 0.800331000 0.259054000 -0.698301000 -0.923619000 -0.488126000 -0.396109000 0.689233000 -0.012999000 -0.783043000 -0.064974000 -0.233059000 -0.909845000 0.626633000 0.736709000 0.138986000 -0.295983000 0.431992000 0.184962000 -0.906869000 -0.089004000 -0.44296000 0.866928000 0.504149000 > 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000000 1.000000000 0.739780000 -0.110030000 0.781108000 0.432846000 0.660036000 0.143059000 0.350073000 0.178077000 -0.139942000 -0.683177000 0.753207000 0.341115000 -0.943903000 0.335018000 -0.790689000 -0.947238000 -0.414929000 > -0.588655000 0.534789000 -0.720927000 0.361979000 0.862984000 -0.978799000 0.301956000 -0.453023000 0.858923000 -0.490959000 -0.025007000 > > Thank you for your help already in advance! > > Regars, Miia Cheers, Stam