new anatomical pipeline

Questions about Anatomist manipulation

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Olivier Coulon
Posts: 176
Joined: Fri Feb 27, 2004 11:48 am
Location: MeCA research group, Institut de Neurosciences de La Timone, Marseille, France
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new anatomical pipeline

Post by Olivier Coulon »

Hello,
I have been using the pipeline05 to process old 'not-so-good' images. I have noticed a strange thing that happens on all images with the default parameters : the brain mask looks like it has been "closed" (morphologically). That is of course propagated to further steps, and even the grey-white interface looks closed or dilated. The bias corection step looks alright, may be the histo analysis is wrong...
I include the snapshots of the different steps of segmentation below. Does it ring a bell, anything already encountered ?
Thanks in advance.

Olivier

T1 :

Image

bias corrected :

Image

histo analysis :

Image

brain mask :

Image

voronoi :

Image

Grey-white interface :

Image

Left and right cortex :

Image
Image
Olivier Coulon
Institut de Neurosciences de La Timone,
Aix-Marseille Université,
Marseille, france
https://meca-brain.org
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Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France
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Post by Jean-Francois Mangin »

Did you try the old pipeline using the bias correction of the pipeline 05?
The other steps are still largely unstable... Can you post one of your scan
somewhere, I will include it in the test database.
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