[MINC-users] rawtominc & nu_correct difficulties

[Audette, Michel]

Hi again Vladimir, 

it worked! This result is as good as anyone can expect. Can you explain to me the significance of the parameters, and why exactly it worked? 

Actually, I may have to go back and redo it with the actual voxel spacing, because the non-rigid registration with patient data, which comes afterward, must be applied to anatomical meshing... but everything scales accordingly, right? 

Cheers, 

Michel


-----Original Message-----
From: Vladimir FONOV [mailto:vladimir.fonov at gmail.com]
Sent: Thu 8/2/2007 5:45 PM
To: Audette, Michel
Cc: Andrew Janke
Subject: Re: [MINC-users] rawtominc & nu_correct difficulties
 
Hello,

On 8/2/07, Audette, Michel <Michel.Audette at medizin.uni-leipzig.de> wrote:
> Hi Vladimir,
>
> thanks for the suggestion. The data is 3D MR microscopy. http://cbaweb2.med.unc.edu/henson_mrm/pages/Scans_Primates.html
>
I tried playing with Human13959, got some success:

rawtominc -byte -range 0 255 -orange 0 255 -real_range 0 255 -unsigned
-zyx -xstep 1 -ystep 1 -zstep 1 -xstart 0 -ystart 0 -zstart 0 -clob
-oshort Human13959_Stack.mnc 176 187 256  < Human13959_Stack.gray

minccalc -expression '255-A[0]' Human13959_Stack.mnc Human13959_Stack_inv.mnc

nu_correct -clob Human13959_Stack_inv.mnc Human13959_Stack_inv_nuc.mnc
-iter 100 -stop 0.0001 -fwhm 0.1

 minccalc -expression 'clamp(255-A[0],0,255)'
Human13959_Stack_inv_nuc.mnc Human13959_Stack_nuc.mnc -clob

see attached images.

P.S. note that I used step size of 1mm instead of 0.025um as indicated
in the dataset

-- 
Best regards,
 Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com