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
>>
>>
