[MINC-users] Conversion to MINC and visual inspection of the MINC-file

[Jörg Pfannmöller]

Dear MINC-Experts,

I am attempting to convert 16 bit images of a mouse brain in tif format (example image attached as number 01) to minc format. Therefore, I use imageJ to convert the original .tif data to .raw data. After that the following command is used to convert the .raw file to an .mnc file:

rawtominc -input t2_3D_tse_3-wt2.raw  -transverse -short -unsigned -ounsigned -xstep 0.0244140625 -ystep 0.0244140625 -zstep 0.10000000149 -mri -origin 0 0 0 -range 0 65535 -real_range 0 65535 -clobber mydata.mnc 96 1024 1024 

Subsequently mydata.mnc is converted to .raw format using:

minctoraw -short -nonormalize mydata.mnc > mydata.raw

This is displayed in imageJ and seem to be correct (example image attached as number 02)

If mydata.mnc is depicted using mincpik:

mincpik -verbose -depth 16 -scale 40 out.mnc MIFF:- | display -

a rather strange image occurs (example image attached as number 03). Since I want to use  out.mnc together with nu_correct I wonder whether the conversion from tif to minc is correctly performed. Sample computations using nu_correct for the reduction of intensity in homogeneities obviously are not correct if displayed with imageJ and converted using 

minctoraw -short -nonormalize nu_correct_result.mnc > nu_correct_result.raw

see example image number 04. Any help would be appreciated

Respectfully yours

                pfannmoe