Hi Samantha,
Your mask is a 4D image rather than the expected 3D image. Rather than run bet on the full diffusion MRI dataset, it is better to extract the single volume you want to actually use to compute the mask.
You can get an average b0 image from your diffusion data using:
$ select_dwi_vols <eddy output data> <bvals file> <output b0 file> 0 -m
You can then get a mask with the right shape by running bet on the output b0 file.
Best wishes,
Michiel
> On 15 Jan 2019, at 12:41, Samantha Baldi <[log in to unmask]> wrote:
>
> Dear FSL users,
>
> I am running FDT to analyse my diffusion data, but I encounter the following error message while running bedpostx:
>
> An error occurred. Please check file .../BEDPOSTX.bedpostX/logs/bedpostx.e18700.1.
>
> Image Exception : #77 :: Cannot use setmatrix() with masks with more than 3 dimensions
>
> Cannot use setmatrix() with masks with more than 3 dimensions
>
> I copy here the output of bedpostx_datacheck so that you can have an idea of the data in my bedpostx input directory:
>
> .../BEDPOSTX/data (output from eddy with outliers correction)
> data_type FLOAT32
> dim1 100
> dim2 100
> dim3 72
> dim4 119
> datatype 16
> pixdim1 2.000000
> pixdim2 2.000000
> pixdim3 2.000000
> pixdim4 1.000000
> cal_max 0.000000
> cal_min 0.000000
> file_type NIFTI-1+
>
> .../nodif_brain_mask (bet on eddy corrected data)
> data_type INT16
> dim1 100
> dim2 100
> dim3 72
> dim4 119
> datatype 4
> pixdim1 2.000000
> pixdim2 2.000000
> pixdim3 2.000000
> pixdim4 1.000000
> cal_max 1.000000
> cal_min 0.000000
> file_type NIFTI-1+
>
> num lines in .../BEDPOSTX/bvals
> 1
> num words in .../bvals
> 119
> num lines in .../bvecs (rotated bvecs after eddy)
> 3
> num words in .../bvecs
> 357
>
> Does anyone know how to solve this problem?
> Thanks in advance for the help, it is highly appreciated
>
> Greetings,
> Samantha Baldi
>
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