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.


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 




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Miao Wei