[MINC-users] Reading minc format DTI data

[Vladimir FONOV]

Hello,

Yonas T. wrote:
> Here is what I found however:
> 
> minctoraw -normalize dti.mnc > ImageData.raw
> Result: ImageData.raw file with size = 227,288,499 bytes  (about 216MB)
> 
> minctoraw -normalize -short dti.mnc > ImageData_Short.raw
> Result: ImageData_Short.raw file with size = 227,288,499 bytes  (about
> 216MB)
> 
> mincextract dti.mnc > ImageDataWithExtract.raw
> Result: ImageDataWithExtract.raw file with size = 2,141,244,230 bytes
> (about 2GB)
> 
> mincextract -normalize -short dti.mnc > ImageDataWithExtract_Short.raw
> Result: ImageDataWithExtract_Short.raw file with size = 225,473,844 bytes
> (about 215MB)

my experiment:

 > mincinfo test_dti.mnc
file: test_dti.mnc
image: signed__ short 0 to 4095
image dimensions: time zspace yspace xspace
     dimension name         length         step        start
     --------------         ------         ----        -----
     time                       32            1            0
     zspace                     40          1.2      -16.894
     yspace                    128     -1.21875      80.1687
     xspace                    128     -1.21875      77.9898

32*40*128*128*4=83886080

 > minctoraw -normalize -float test_dti.mnc > test1.raw
 > mincextract -float test_dti.mnc > test2.raw
 > ls -l test1.raw test2.raw
-rw-r--r-- 1 vfonov pet 83886080 Jun 21 18:41 test1.raw
-rw-r--r-- 1 vfonov pet 83886080 Jun 21 18:41 test2.raw

 > cmp  test1.raw test2.raw

(no messages, meaning files are identical)


> So my questions,
> 
> 1. As you can see from the result, I am baffled by these strangely different
> results when using minctoraw versus mincextract calls. Worse, none of these
> file sizes matches what I expected. That is the file size is LARGER than
> what I expected (mincextract -normalize -short dti.mnc >
> ImageDataWithExtract_Short.raw gives 225,473,844 bytes although I expected
> 225,017,856 bytes). Any idea, please?
> 
> 2. I also found emma matlab toolbox that can read minc format images. Going
> through line by line of the reading routines, I can see that this tool does
> nothing but uses mincextract to read the minc file to a temporary file and
> then takes the first N bytes (where N is the expected size) from the
> temporary file and returns. That is although the temporary file is bigger,
> what emma does is simply discard the extra bytes. My questions here is: does
> this emma knows the extra bytes are at the end of the raw file read? Is
> there any documentation for this?

As far as I know emma is unsupported now.


> 
> 3. Does the result of mincinfo seem meaningful? I am a bit surprised by "image:
> signed__ short 0 to 4095" because I would think unsigned short would make
> more sense to say range 0 - 4095.

2**12=4096 - so scanner have got 12bit ADC I suppose ?


> Any ideas please? Or any better way to read minc format image to save it as
> raw file?

You can try to use niak: http://code.google.com/p/niak/ , it uses 
mincextract internally as well.


-- 
Best regards,
  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info