Front Page Forums BioMap Mapping mz values in t2m files to img intensities Re:Mapping mz values in t2m files to img intensities

Ralf Tautenhahn

I am having the same problem. I cannot find out the how to match the t2m to the image dimensions.
The 4800 imaging tool was used.

In my example, the filesize is

Image dimension as reported by nifti-tools are:

$ nifti_tool -disp_hdr -infiles img.hdr
name offset nvals values
——————- —— —– ——
dim 40 8 4 15250 424 152 1 0 0 0
datatype 70 1 4

The number of values int the t2m file is 80786 (file size 323144).

So the number of values is the t2m is 80786/15250 = 5.297443 times higher than the data dimension.

The datatype is 4 = signed short = 2 bytes
According to the file size 10412992256 / (424 * 152) / 2 bytes = 80786

So it looks like the data dimension is 80786 (and not 15250), which would make sense with the t2m file. I understand that dimensionfor the ANALYZE format is limited to 32768 and it therefore shows a different value in the header.

But how can datatype 4,signed short, 2 bytes (2^16=65536) address 80786 m/z indices ?
I guess, binning is used ?
How can I find out the binning details (offset, bin size) ?

Thank you for your help!


PS: Is there any plan to support imzML as an output format for the imaging tools ?
That would be really helpful and get rid of all these limitations of the ANALYZE file format.