>Thanks. May I ask you a few more questions:
I got the undistorted 4D DTI brain output from FEAT GUI
(filtered_func_data.nii.gz) which looks good. However, it is deskulled and
has less brain tissue compared to the undistorted 3D DWI brain output
which is not deskulled (EF_UD_example_func.nii.gz in unwarp subfolder).
The loss of brain tissue due to masking is quite visible in the inferior
temporal lobe, which is the region I'm interested in. I have betted the
magnitude file very liberally but the problem remains. I assume this is
used to mask/bet the 4D data. Is there a default 4D undistorted brain
output which is not deskulled from running the B0 unwarping function in
FEAT GUI, as I couldn't locate it? If there isn't, what other ways can be
done to lessen the tissue lost in the undistorted 4D DWI brain output?
Secondly, is there a benefit to apply FWHM spatial smoothing when carrying
out only the B0 unwarping function on DTI data?
Lastly, if I have two repetition/ acquisitions of 4D DWI, do you suggest
it's better to perform the B0 undistortion on them seperately, before
averaging them?
Thanks
Siewmin
Hi,
>
> I'm not sure why the intensity range is different in your nifti
> image, but use that range. It is more likely that the reconstruction
> software tries to use the range 0 to (2^n - 1) for the intensity
> range. Hence you should map the range 2048 to 2*pi. You
> could also argue that 2047 is better - but the difference, which
> is less than 0.05% won't affect anything significantly, given
> the typical SNR in MR images.
>
> All the best,
> Mark
>
>
>
>
> On 11 May 2009, at 21:39, Siew-Min Gan wrote:
>
>> Hi, on the fsl practical page, there is a step on preparing phase
>> difference map to a fieldmap in rad/sec with the following command
>> "fslmaths phasemap -sub 2048 -div 2048 -mul 3.14159 phase_rad -odt
>> float".
>>
>> When I look at the histogram of the intensity of the phasedif map, the
>> dicom file has a range of intensity from -4096 to 4092. In nifti
>> format,
>> it's intensity range is 0 to 4094. May I ask if it is more accurate
>> to
>> keep to 2048 or to substitute 2048 to 2047 in the above calculation?
>>
>> Thanks
>>
>> Siewmin
>>
>
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