[MINC-users] FW: rawtominc difficulties

Tue Jul 31 12:25:26 EDT 2007

<160E3DD4FB702C4CB860C65186686E69011455D8 at MRZS152229.medizin.uni-leipzig.de> <46AF54DF.9090902 at bic.mni.mcgill.ca> <160E3DD4FB702C4CB860C65186686E69011455DB at MRZS152229.medizin.uni-leipzig.de>
From: "Audette, Michel" <Michel.Audette at medizin.uni-leipzig.de>
To: <minc-users at bic.mni.mcgill.ca>

Dear Jason and Andrew, 

thanks for your kind and incredibly prompt replies. Jason, your advise was bang on, although I had to permute the sizes for the various axes. I have a volume, although it look like it can use some serious post-processing (one slice appears significantly corrupted, and the volume seems to exhibit quite a lot of intensity nonuniformity). 

Thanks again gents. 

Michel

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Jason Lerch
Sent: Tue 7/31/2007 5:27 PM
To: MINC users mailing list
Subject: Re: [MINC-users] rawtominc difficulties

Try something like the following:

convert -depth 8 tifffile.tif rawfile.gray
cat rawfile.gray | rawtominc -clobber output.mnc 489 366 340

(the -depth in convert is often key)

Jason

Audette, Michel wrote:
> Dear all, 
>
> 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.
>
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 1 489 366 -input HumanS16885_Stack.raw
> maudette at icaw164201:~/data/ENTdata> rawtominc -clobber HumanS16885_Stack.mnc 2 489 366 -input HumanS16885_Stack.raw
> rawtominc: Premature end of file.
>
> The following is my tiffinfo result, for the tiff file that produced the raw file. 
>
> maudette at icaw164201:~/data/ENTdata> !tiff
> tiffinfo HumanS16885_Stack.tiff
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: unknown field with tag 43314 (0xa932) encountered.
> TIFF Directory at offset 0x8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>   Compression Scheme: None
>   Photometric Interpretation: min-is-white
>   Samples/Pixel: 1
>   Rows/Strip: 366
>   Planar Configuration: single image plane
>   Tag 43314: 18768,18755,18765,16711,366,489,162,768,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,65535,0,0,0,65535,0,0,0,65535,65535,65535,0,0,65535,65535,65535,0,65535,0,255,0,0,0,0,0,0,0,14,0,0,255,255,0,2,16605,15543,42740,56988,49245,30630,62686,39891,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,100,150,16256,0,340,0,0,4,0,0,16256,0,0,255,256,65535,65535,65535,0,0,0,3,0,1392,27000,25964,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
> TIFFReadDirectory: Warning, HumanS16885_Stack.tiff: TIFF directory is missing required "StripByteCounts" field, calculating from imagelength.
> TIFF Directory at offset 0x3a086d8
>   Subfile Type: (0 = 0x0)
>   Image Width: 489 Image Length: 366
>   Bits/Sample: 8
>
> When I did a tiff2pdf I saw that the pdf file looked fine, and had 340 pages. 
>
> Can anyone suggest how to proceed? Is there a way of checking that my raw file was properly converted from tiff, to begin with?
>
> Thanks for your kind consideration. 
>
> 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
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   

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