>I have tried setting the Brain/Background threshold to 0% as well as the
default at 10%. Should it be set at 0% or 10%? I have left the balloon
help, progress watcher turned off and the other numbers in the design
efficiency box as it is. There is no difference in the results. The
filtered_func_data.nii.gz, the only 4D undistorted DWI output is still
deskulled with some area lost as described. The only thing I haven't
mentioned is that when I try to fslview this filtered_func_data.nii.gz
file (4D undistorted DWI) or the example_func.nii.gz file (3D undistorted
DWI)in the folder filename.feat, I can view it but get an error message
"ERROR (nifti_image_read): failed to find header file for
'/xxmyfilename/filename.feat/stats/pe1'
This error message is resolved if I copy these file outside the .feat
folder before viewing them. Apart from this, everything seems to be
working ok. Where else do you think I could have done wrong and hence did
not get a 4D DWI undistorted brain with skull on in the
filtered_func_data.nii.gz file?
Thanks
Siewmin
Hi,
>
> Just to check - have you set the Brain/Background threshold
> to 0% in the "Misc" tab on the Feat GUI?
>
> All the best,
> Mark
>
>
> On 7 May 2009, at 18:40, Siewmin Gan wrote:
>
>> Hi,
>> I would like to ask if the magnitude_brain (betted Magnitude map)
>> is used to mask the
>> 4D DTI DATA when running FEAT GUI to do B0 distortion correction?
>>
>> I have run a few samples on FEAT GUI to do only the B0 distortion
>> correction on DTI data.
>> However, in the output folder, the only 4D DTI undistorted output
>> available has been
>> bettted, and there are some area lost in the inferior temporal lobe
>> region. I have re-
>> betted the Magnitude map liberally at a threshold of 0.15, before
>> inputting the
>> Magnitude_brain file to run this function in the FEAT GUI.
>> Everything is turned off in the
>> prestats section including the "BET brain extraction" option.
>> However, this problem
>> remains. Is there any way to resolve this? or to get an undistorted
>> 4D DTI output file that
>> is not already betted?
>>
>> I performed tractography on the original distorted dti data and the
>> betted undistorted dti
>> data, and for a few tracts from the temporal lobe, their volume is
>> less when derived from
>> the betted undistorted dti, so I'm not sure if it's due to the
>> "lost" area in the betted
>> undistorted dti, or the undistorted effect.
>>
>> Many Thanks
>>
>> Siewmin
>>
>
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