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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.


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!!



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Miao Wei 



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Miao Wei 




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Miao Wei 




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Miao Wei