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Dear Jesper, Sorry for the deplayed reply, since there was something wrong with my computer. I checked the qform/storm in these three b0 images, and found that qform of b0_19.nii.gz image scanned by the 19 orientation gradient table was different from the other two. I listed them below. Is there any way for me to solve this problem? (1) b0_19 orientations: qto_xyz:1 -1.718750 0.000000 -0.000000 109.325317qto_xyz:2 0.000000 1.691586 -0.301044 -80.299522qto_xyz:3 0.000000 0.304364 1.673132 -40.676346 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 (2) b0_20/21 orientations: qto_xyz:1 -1.718750 0.000000 -0.000000 107.975891qto_xyz:2 0.000000 1.691586 -0.301044 -81.648949qto_xyz:3 0.000000 0.304364 1.673132 -40.676346 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 Their sform are same. sform_xorient: Right-to-Leftsform_yorient: Posterior-to-Anterior sform_zorient: Inferior-to-Superior Thanks so much for your concern! Yours, Lulu 2013/10/7 Jesper Andersson <[log in to unmask]> > Dear Lulu, > > I was trying to do pre-processing with our high angular resolution > diffusion data from Siemens 3T.The acquisition was divided into 3 > consecutive scans of 5 minutes each, to improve the comfort of the subject. > They consisted of three blocks of 19, 20 and 21 orientations each. Each of > these three acquisitions have one b0 images. > I read the manual of fsl's tool 'eddy' and 'topup', and I think that our > data could be correctd(eddy current and suscepbility problem) by these two > tools (Am I right?). > I extracted three b0 images, and tring to merge them together, but it gave > me an error: > > 'fslMerge fault:Inconsistent orientations for individual images when > attempting to merge. > Merge will use voxel-based orientation which is probably incorrect > -*PLEASE CHECK*!' > > I am not sure that if this problem is related to my gradient > orientation, and if this problem would influence my following processing. > > > I don't think this has to do with your gradient directions. It sounds > either like a round off error in the voxel size fields, or the storm/qform > is different. I suggest you use fslhd to check those things. > > Another problem is about the acqparams.txt file. Since we have three > b0 images, and our phase encoding direction is R>>L, EPI factor is 128, > echo spacing is 0.85 ms, I wrote the acqparams.txt file like this > " 1 0 0 0.108 > -1 0 0 0.108 > 1 0 0 0.108 > -1 0 0 0.108 > 1 0 0 0.108 > -1 0 0 0.108" > Is this the right way to write the acqparams file for our three b0 images? > > > There is documentation about how to write these here > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq and here > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY/Faq. > > However, it is not clear from your description if you acquired b=0 scans > with reversed phase encode blips. Your acqparams file implies you have six > b=0 files acquired R->L, L->R, R->L, L->R, R->L, L->R in that order. Is > that correct? > > Jesper > > > Thanks in advance! > > Lulu > > > >