Hi Doug,
I am using reg-feat2anat on the feat directory of each run.
reg-feat2anat --feat feadir.feat --subject XX
Then I checked and adjusted the registration with:
reg-feat2anat --feat featdir.feat --manual
Next I checked and adjusted the registration to the standard with:
reg-feat2anat --feat featdir.feat --manxfm func2std
To generate cortical binary masks I used:
aparc2feat --feat featdir.feat --annot BA
fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 10
featdir.feat/reg/freesurfer/V1_l.nii.gz
To generate subcortical binary masks I did:
aseg2feat --feat featdir.feat --aseg aparc+aseg
fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 -uthr 54
featdir.feat/reg/freesurfer/amygdala_r.nii.gz
When I looked at the masks in FSLview and checked the masks against the
other atlases, everything was off even after painstakingly editing the
registrations.
Is there something I am doing wrong?
Thanks.
Michelle
On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu>wrote:
> How are you generating the masks?
> doug
>
> Michelle Umali wrote:
>
>> Hi Freesurfers,
>> I've run reg-feat2anat on several subjects in order to generate binary
>> masks to use in an FSL ppi.
>> For 3 subjects, this completely failed.
>>
>> When I looked at the fsl's own registration of fsl feat 2 standard (via
>> tkregister2), the registration is fine, but after running reg-feat2anat, the
>> registration of the feat to the freesurfer anatomical and the feat to
>> standard are completely off.
>>
>> I manually fixed and saved the registration edits via reg-feat2anat
>> --manual, but when I generated the masks again, they were totally wrong
>> still.
>> When looking at freesurfer's feat to standard registration, it looks like
>> all the brains weren't tall enough in the saggital view. Am I supposed to
>> stretch the feat brain to fit?
>>
>> How can I fix this so that the masks are accurate?
>>
>> Thanks.
>> Michelle
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>
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> MGH-NMR Center
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