[MINC-users] Reading minc format DTI data

[Andrew Janke]

Hi Yonas,

On Tue, Jun 22, 2010 at 08:24, Yonas T. <yonas.t at gmail.com> wrote:
> I am trying to read DTI data that is stored in minc file format (minc 1.0 I
> am told). I am using PC and found this win32 binary distribution at:
> http://packages.bic.mni.mcgill.ca/win32/

Erk! for one, these binaries are very old, but might suffice for what
you are doing.

>    time                            109         11.1            0
>    zspace                        63           -2      69.2799
>    yspace                       128           -2      189.266
>    xspace                       128           -2          128

> Now, I would like to read ONLY the image part (no header information) and
> save it as raw file so that I can read it in matlab; as my code for the
> analysis of DTI is developed in matlab.


> Here is what I found however:
> minctoraw -normalize dti.mnc > ImageData.raw
> Result: ImageData.raw file with size = 227,288,499 bytes  (about 216MB)

To add to what others have said here, what version of windows are you
using? I have found binary redirects and pipes of large files to be
somewhat hit and miss under XP at least. Under cygwin things seem to
work better though. I have no idea why this is as I very rarely use
windows for such things.

> 2. I also found emma matlab toolbox that can read minc format images

I would suggest (as Vlad said) to use NIAK:

   http://code.google.com/p/niak/

Unlike EMMA it is under active development.

> 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.

This is normal for a image from a scanner, the image is saved in a 16
bit filetype but most ADC's in scanners are only accurate to about 12
bits so the output is truncated. DICOM also stores 12 bit imaging data
in this format.


--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883