[MINC-users] rawtominc & nu_correct difficulties

[Audette, Michel]

Dear folks, 

subsequent to yesterday's discussion, I'm trying to run nu_correct on a volume converted from tiff to raw to minc, as the volume has significant intensity inhomogeneity, but there is apparently something that I've neglected to do in the conversion. See below, where I've used some of Vladimir Fonov's parameters.  

maudette at icaw164201:~/data/ENTdata> cat HumanS16885_Stack.gray | rawtominc -clobber -byte -range 0 255 -orange 0 255 -real_range 0 255 -unsigned -zyx HumanS16885_Stack2.mnc 340 366 489
maudette at icaw164201:~/data/ENTdata> nu_correct  HumanS16885_Stack2.mnc HumanS16885_Stack2_nuc.mnc
nu_estimate_np_and_em: crashed while running volume_stats (termination status=11)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)

Can anyone spot the missing parameter? The program nu_correct otherwise runs fine on other MINC volumes, which have been converted from DICOM. 

Cheers, 

Michel

Michel Audette, Ph.D.
Innovation Center Computer Assisted Surgery (ICCAS)
Philipp-Rosenthal-Strasse 55
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 on behalf of Audette, Michel
Sent: Tue 7/31/2007 6:17 PM
To: MINC users mailing list; vladimir.fonov at gmail.com
Subject: Re: [MINC-users] rawtominc difficulties
 
Hi Vladimir, 

thanks to you too for the tip. 

Cheers, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Vladimir FONOV
Sent: Tue 7/31/2007 6:00 PM
To: MINC users mailing list
Subject: Re: [MINC-users] rawtominc difficulties
 
Hello,

On 7/31/07, Audette, Michel <Michel.Audette at medizin.uni-leipzig.de> wrote:
> when I try to perform a rawtominc, with any slice number larger than 1, I get rawtominc: Premature end of file.
> See below:
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 1 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 489 366 2 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
> Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
>
You can check the size of the file , for example. If there are no
headers, it should be
X*Y*Z bytes long .

Also, when i was using rawtominc i was explicitly specifying some things:
rawtominc -byte -range 0 255 -orange 0 255 -real_range 0 255 -unsigned
-zyx  ....



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