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Hi Khoi, I followed these steps and now DTIFIT will work. Thanks a lot. Miao 2017-08-24 17:42 GMT-07:00 Khôi Huỳnh <[log in to unmask]>: > Hi, > > You can use fslsplit to get the b0 image (usually it is the first volume > i.e vol0000.nii.gz). Then use BET on that image, please add the -m option > to have it generate a binary mask. > > The next step is to use fslmaths <4D-DTIdata> -mul <Binarymask> <Output> > to have it masked. > > Best, > Khoi > > On Thu, Aug 24, 2017 at 6:33 PM, Iris Wei <[log in to unmask]> wrote: > >> I think I BET the 4D data, but I can't find a place to change BET's >> setting to not change my volume number of the data. Then how to run BET >> only on the B0 image and used binary mask to mask the whole 4D data? >> Thanks!! >> Miao >> >> 2017-08-24 15:03 GMT-07:00 Khôi Huỳnh <[log in to unmask]>: >> >>> Hi, >>> >>> Then please check your BET procedure. Did you apply BET on 4D data or >>> just the initial B0 image only? I personally would run BET on the B0 image >>> and use the binary mask to mask the whole 4D data. >>> >>> best, >>> Khoi >>> >>> On Aug 24, 2017, at 5:56 PM, Iris Wei <[log in to unmask]> wrote: >>> >>> Hi Khoi, >>> I just reran dicom2nii again and i found out that the DTI data after >>> conversion is 33 volumes and after eddy it is 33 volumes, but after I ran >>> BET on it, it change to 1 volume. >>> I checked the volume using fslnvols. >>> Miao >>> >>> 2017-08-24 14:35 GMT-07:00 Khôi Huỳnh <[log in to unmask]>: >>> >>>> Hi, >>>> >>>> Could you run it again. Usually, I have no problem from running dcm2nii >>>> to convert the data. >>>> >>>> https://www.nitrc.org/frs/shownotes.php?release_id=1855 >>>> >>>> best, >>>> Khoi >>>> >>>> On Aug 24, 2017, at 5:27 PM, Iris Wei <[log in to unmask]> wrote: >>>> >>>> just checked and how come it is one. I used dicom2nii to convert my DWI >>>> data to nifti. >>>> it is one volume? >>>> then how do I fix this? >>>> >>>> 2017-08-24 14:22 GMT-07:00 Khôi Huỳnh <[log in to unmask]>: >>>> >>>>> Hi, >>>>> >>>>> Could you confirm the result of fslnvols <yourdata> is 33 ? >>>>> >>>>> best, >>>>> Khoi >>>>> >>>>> On Aug 24, 2017, at 5:14 PM, Iris Wei <[log in to unmask]> wrote: >>>>> >>>>> And I got my bval and bvec from running dicom2nii. How come it does >>>>> not match my data? >>>>> >>>>> 2017-08-24 14:12 GMT-07:00 Iris Wei <[log in to unmask]>: >>>>> >>>>>> Hi Khoi, >>>>>> Thanks so much for replying. >>>>>> So I attached my bval and bvec with this email and I noticed my bval >>>>>> start from 0 and then 800,... >>>>>> How do I fix this and have DTIFIT to run so that I can continue my >>>>>> analysis? >>>>>> Thanks. >>>>>> Miao >>>>>> >>>>>> 2017-08-24 13:31 GMT-07:00 Khôi Huỳnh <[log in to unmask]>: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> The volume counter in FSLeyes starts at 0. Hence, if your last >>>>>>> volume number is 33, probably that the data has 34 volumes. >>>>>>> >>>>>>> best, >>>>>>> Khoi >>>>>>> >>>>>>> > On Aug 24, 2017, at 4:27 PM, miao Wei <[log in to unmask]> >>>>>>> wrote: >>>>>>> > >>>>>>> > To whom it may concern, >>>>>>> > I submitted a question regarding error message of dtifit yesterday >>>>>>> but was not lucky enough to get a response. >>>>>>> > So I went ahead and checked for my bvec and bval files. Both of >>>>>>> them has 33 entries. >>>>>>> > I used FSLeyes to look at my DTI data and dimension 4 listed as 33 >>>>>>> as well. Does this means that I also have 33 volumes? >>>>>>> > If so why when I run DTIFIT it still give me the error message as >>>>>>> 'Errors: data and bvals/bvecs do not contain the same number of entries'. >>>>>>> > I am so confused and could use any hint or help. Thank you!! >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Miao Wei >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Miao Wei >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Miao Wei >>>> >>>> >>>> >>> >>> >>> -- >>> Miao Wei >>> >>> >>> >> >> >> -- >> Miao Wei >> > > -- Miao Wei