[MINC-users] rawtominc & nu_correct difficulties

[Audette, Michel]

Dear all, 

a while back, when I was dealing with an inner ear micro-MR model, some of you suggested that I change the header to 1mm resolution, nu_correct it, then change it back to its original resolution. And it worked terrifically.

I now have a large pelvic volume (I have several simulation projects here...), of 7T data 0.33x0.33x0.5mm voxels, in other words, much larger than the head, and finer than 1mm isotropic voxels. Can you suggest how to proceed? The inhomogeneity is very significant... 

Best regards, 

Michel

Michel Audette, Ph.D.   
Innovation Center Computer Assisted Surgery (ICCAS)   
Semmelweisstraße 14  
Leipzig, Germany  
Phone: ++49 (0) 341 / 97 - 1 20 13  
Fax: ++49 (0) 341 / 97 - 1 20 09 
 

 

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Audette, Michel
Sent: August 2, 2007 6:26 PM
To: Vladimir FONOV
Cc: minc-users at bic.mni.mcgill.ca; Andrew Janke
Subject: Re: [MINC-users] rawtominc & nu_correct difficulties

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


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