[MINC-users] Automated Segmentation Questions

[D. Louis Collins]

Paul,

The procedure described on my web site is still valid, however, many of 
the programs have been updated and yield better results now.

Answers are below.

-Louis


On Jun 21, 2004, at 11:07 AM, Paul GRAVEL wrote:

> 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?

pretty much.  ANIMAL now uses the ICBM152 model for more robust linear 
registrations.

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

this is based on N3, the method of John Sled.

> 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?

classify_clean is a perl script that uses both bayesian and artificial 
neural nets for classification and is based on INSECT.

> 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?

step 5, stx_segment, takes the output of the linear and non-linear 
registrations and combines it with the classified data to achieve a 
segmentation.  The entire procedure, registrations+classifications is 
ANIMAL.

Hope this helps,

-L


>
> 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
>
>
>
>
> _______________________________________________
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