Could you send me a picture of the segmentation and underlying image?
Cheers,
Brian
> Thanks Brian,
>
> I tried bias field correction prior to FIRST as you described. There is
> some
> improvement but there is still a significant amount of tissue missing.
>
> Best
> Deniz
>
> On Wed, 26 Aug 2009 23:47:54 +0100, Brian Patenaude
> <[log in to unmask]> wrote:
>
>>Hi,
>>
>>There is actually many children in the training set used to create the
>>model. Is there any difference in presence of bias field effects between
>>the adults and children? You could try running
>>
>>brain extracting -> bias field estimation with FAST -> apply correction
>> to
>>whole head image -> the run FIRST
>>
>>Cheers,
>>
>>Brian
>>
>>> Hi,
>>>
>>> I am trying to segment cerebellum using FIRST on small group of
>>> subjects
>>> that
>>> consists of adults and children. I am really impressed by the
>>> segmentation
>>> that
>>> I get on adults, but the segmentation on children images are
>>> underestimating
>>> the cerebellum by about 5 mm towards the bottom and sides.
>>>
>>> I was wondering if there are any parameters I can adjust, or different
>>> models
>>> that are available for children.
>>>
>>> I am using the following commands to get the segmentation. (I believe
>>> somebody has posted these here a few months ago, thanks :) ). "T1"
>>> refers
>>> to
>>> an MPRAGE sequence, it is *not* brain stripped.
>>>
>>> Thanks in advance for any input you can provide.
>>>
>>> Deniz.
>>>
>>> run_first_all -i T1.nii.gz -o T1_out
>>>
>>> first_flirt T1 T1_to_std_sub -cort
>>> run_first -i T1 -t T1_to_std_sub_cort.mat -n 40 -o T1_R_Cereb -m
>>> ${FSLDIR}/data/first/models_336_bin/intref_puta/R_Cereb.bmv -intref
>>> ${FSLDIR}/data/first/models_336_bin/05mm/R_Puta_05mm.bmv
>>> first_boundary_corr -s T1_R_Cereb -i T1 -b fast -o T1_R_Cereb_corrected
>>>
>>>
>
>
