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I don't have personal experience on Siemens scanner but based on some online database it shouldn't. However, they may change it as developing of their scanners. You may read the last volume and compare it to your B0 volume and other volumes to know whether it is B0 or ADC. On Sat, Oct 2, 2010 at 10:26 PM, Yuhong Liu <[log in to unmask]> wrote: > Thank you very much, Xiaowei > > It is Siemens scanner. In my case, does the gradient vector (0 0 0) and b > = 800 in the last volume mean that it is ADC volume? > Best > > Shugao > On Sat, Oct 2, 2010 at 3:41 PM, vivian <[log in to unmask]>wrote: > >> >> Hi Yuhong, >> >> Is it a Philips scanner? If so, the last volunme is ADC volume. For detail >> you could refer to some Philips document. They use this to do fiber track on >> scanner. >> >> For your bvecs and bvalues, it may due to some txt formate. for example, >> after you manually deleted the last entry, it may add 0 at the end of file >> when it is read in FSL/MATLAB. I'm nost sure since I've never tried before. >> you may want to read the file into MATLAB to check whether something >> changed. >> >> >> On Fri, Oct 1, 2010 at 9:40 PM, Yuhong Liu <[log in to unmask]> wrote: >> >>> Dear FSL experts: >>> >>> >>> >>> I am new fsl users, I have some questions. >>> >>> >>> I generated FA image by following the following steps >>> 1: eddy_correct >>> 2: Bet, threshod 0.5 >>> 3: dtifit >>> >>> >>> In the generated FA image, there are very high intensity in the brain >>> boundary, and there are some voxels FA > 1, see the attached figure. The >>> FA image seems to look unclear. >>> >>> >>> I used DWIs of the 32 directions to generate FA. I converted decom to >>> .img (.hdr) by MRIConvert. There are 34 volumes in this 4D image, and I >>> checked bvecs and bvals (see the attached file) and found: >>> the last gradient direction in bvecs is 0 0 0, and the last value in >>> bvals is 800, I am not sure that these files are correct. >>> >>> >>> But I delete the last volume in 4D image, remove the last gradient >>> direction (0 0 0 ) in bvecs and the last b = 800 in bvals, but I got errors >>> in ditfit: >>> Errors: bvecs and bvals don't have the same number of entries. >>> >>> >>> why? I removed the last gradient direction in bvecs and b value in bvals, >>> respectively. >>> >>> >>> I saw many old archives that we can use rotate_bvecs to rotate the bvecs >>> after eddy_correct. Is it necessary? >>> I didn't find such command in fsl ( I uses v4.10 version) . If >>> rotate_bvecs is necessary, how should I do? >>> >>> >>> Any comments, Thank you in advance >>> >>> >>> Best >>> >>> >>> Shugao >>> >> >> >> >> -- >> Xiaowei.Zou >> >> Department of Biomedical Engineering >> Columbia University >> New York, NY, 10027 >> >> > -- Xiaowei.Zou Department of Biomedical Engineering Columbia University New York, NY, 10027