[MINC-users] Automated Segmentation Questions

[Paul GRAVEL]

Hi All,

I am not sure if this is the appropriate mailing list to send these
questions(bottom of e-mail) to, but I will ask them anyway.  Please let me
know if I should send them to another mailing list.

I have 42 subjects that I needed to segment into several ROI's.
I used the procedure displayed on Dr. Louis Collins Web Page
(http://www.bic.mni.mcgill.ca/users/louis/pet_segment)

The procedure is as followed:

Step 1: mritotal $arg1'_mri.mnc' $arg1'_mri_stx_lin.xfm'

Step 2: nu_correct $arg1'_mri.mnc' $arg1'_mri_nuc.mnc'

Step 3: mritotal -nonlinear $arg1'_mri_nuc.mnc' -transformation
$arg1'_mri_stx_lin.xfm' $arg1'_mri_stx_nonlin.xfm'

Step 4a: mincresample -like /avgbrain/brain/images/icbm_template_1.00mm.mnc
$arg1'_mri_nuc.mnc' -transformation $arg1'_mri_stx_lin.xfm'
$arg1'_mri_stx_nuc.mnc'

Step 4b: classify_clean $arg1'_mri_stx_nuc.mnc' $arg1'_mri_stx_classes.mnc'

Step 5: stx_segment $arg1'_mri_stx_nonlin.xfm' $arg1'_mri_stx_lin.xfm'
$arg1'_mri_stx_classes.mnc' $arg1'_mri_stx_labels.mnc'


My questions are as followed:

1 - Is this still the best procedure to do segmentation?

2 - Is step 2(nu_correct) based on the N3 Algorithm, if not which
algorithm is it based on?

3 - Is step 4b(classify_clean) based on the INSECT (Intensity Normalized
Stereotaxic Environment for the Classification of Tissue) Algorithm, if
not which algorithm is it based on?

4 - Is step 5(stx_segment) based on the ANIMAL (Automatic Nonlinear
Imaging Matching and Anatomical Labelling) Algorithm, if not which
algorithm is it based on?

I thank you very much in advance.

Best Regards,

Paul
______________________________

Paul Gravel
Neurobiological Psychiatry Unit
McGill University
1033 Pine Avenue West
Montreal, Quebec, Canada, H3A 1A1
Phone:  (514) 398-7301
Fax:    (514) 398-4866