[MINC-users] Would you have a MINC tool to extract sulci from a gad-enhanced T1?

[Laurence Mercier]

Hello minc-users,

I would like to know if one of you has coded a tool to extract the sulci 
from a gad-enhanced T1? I am programming a script to convert a 
gad-enhanced T1 MRI into an ultrasound looking image. In ultrasound, the 
  sulci look very bright and I need to model that.

I programmed some sort of a hack, but it is not very elegant and I was 
wondering if anyone would have something better.

My version works as follows:

I get the CSF map with classify_clean. I then attempt to remove the 
ventricles from there to only keep the CSF in the sulci. As the 
ventricles of the patients I work on are far from normal (patients with 
large tumors) I have to dilate the ventricle mask that I get because for 
my application it is very important not to have any "false sulci".

In attachment you can see the result (sulci in red) which is not bad, 
but is still not sensitive enough.

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For those that prefer the code, it goes as follows:

#Dilate ventricles to make sure they all connect
do_cmd("mincchamfer $ventricles_mask ventricles_mask_chamfer.mnc");
do_cmd("minccalc -expression 'if(A[0]>6){1}else{0}' 
ventricles_mask_chamfer.mnc larger_ventricles_inv.mnc");
do_cmd("mincmath -not larger_ventricles_inv.mnc larger_ventricles.mnc");

#Add that to the csf map
do_cmd("mincmath -seg -const2 1 1 $classif_tal csf_map.mnc -clob");
do_cmd("mincmath -or larger_ventricles.mnc csf_map.mnc 
csf_map_larger_vent.mnc");

#Only keep the largest connected group
#ED is needed in order to diminish the number of groups, otherwise there 
are more than 256
do_cmd("mincmorph -successive 'EDB[0.5:1.5:1:0]GB[0.5:1.5:1:0]' 
csf_map_larger_vent.mnc final_vent_mask.mnc");

#Substract ventricles from csf to keep the sulci only
do_cmd("minccalc -expression 'if(A[0]>0.5 && A[1]>0.5){0}else{A[0]}' 
csf_map.mnc final_vent_mask.mnc sulci_mask.mnc -clob");
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Thanks for your help!

Laurence


-- 
Laurence Mercier
McConnell Brain Imaging Center
Montreal Neurological Institute, room: WB-320
3801 University St
Montreal (QC), H3A 2B4
CANADA

Office Phone: +1 514.398.1573
Office FAX: +1 514.398.2975
Web: http://www.bic.mni.mcgill.ca/~laurence