On 7 Jan 2019, at 20:26, Chris Watson <[log in to unmask]> wrote:

Yes, I uploaded the file as "watson_dwi_orig.nii.gz". I also uploaded b0_fsl5 and b0_fsl6

The command line call was simply:

fslroi dwi_orig b0_fsl6 0 1

Thanks,

Chris

On Mon, Jan 7, 2019 at 6:54 AM Matthew Webster <[log in to unmask]> wrote:

Hi,

  Can you upload your original input file to https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF so we can have a look at it? Also can you let me know the exact fslroi command line call?

Kind Regards

Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 5 Jan 2019, at 20:48, Chris Watson <[log in to unmask]> wrote:

Hi, I have some Philips 3T (Intera) diffusion images for which I am using "fslroi" to get the b0 image. I see different behavior in FSL6 compared to FSL5.0.9:

1) the output datatype is different. The DWI volume is INT16, and "fslroi" returns INT16 (FSL6) or FLOAT32 (FSL5).
2) the voxel value ranges are drastically different:

$ fslstats dwi_orig -r
0.000000    65674.257812

$ fslstats b0_fsl6 -r
-28676.478516    28226.824219

$ fslstats b0_fsl5 -r
0.000000    173521.359375

I did the same thing, extracting the first volume of a 4D resting-state fMRI series, but the output was (nearly) identical.

I can't figure out what the issue is. This is on CentOS 7.4.1708; GCC 5.4.0; openblas 0.3.4

I am happy to provide any other information.

Chris

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