Dear SPMer,
I read the following explanation Dr. Matthew Brett gave regarding 'scale
factor' in the header file, but I still couldn't quite understand it.
SPM[96] HELP says that 'a scaling coefficient' is applied during memory
mapping [SCALE]. What exactly does 'memory mapping' do? And how is the
scale factor applied?
I'd like to know if 'scale factor' is related to the value of each voxel.
Since after relignment in SPM96, I'd like to process images by using my
own C-programs. I can use 'fread' in C to get data from '*.img', but I am
not sure if the value got directly from 'fread' is real, or, the real
value of each voxel equals to 'scale factor' by the value got from
'fread'??
We have a set of realigned files 'r*.img', and all of them have the same
scaling=0.8706, after I use 'MEAN' under SPM96, the scale
factor in 'average.hdr' becomes 0.7762; But if I use 'MEAN' under
SPM95, the scale factor in 'average.hdr' is still 0.8706. Could you tell
me how SPM96 gets the value for the scale factor in header file?
Thanks very much for any helps!
Ning Ma
Maryland Psychiatric Research Center
University of Maryland at Baltimore
tel. 410-719-6816
>From [log in to unmask] Tue Dec 15 11:21:25 1998
Date: Thu, 10 Dec 1998 21:54:05 GMT
From: Matthew Brett <[log in to unmask]>
To: [log in to unmask]
Cc: [log in to unmask]
Subject: Re: About the header files
Dear Jack,
> I am looking for some information about the header files structure.
> Could anybody tell me about the scale and the origin position and
> description in the header files since the analyse format description
> avalable at the Analyse site doesn't mention it
> (http://turboguide.com/data2/cdprod1/doc/software.frame/001/160.pub.Mayo.Fou
> ndation.html).
> The most puzzeling factor for me is the scale factor, but reading the
> mails, it seems that it is only concerning PET data. How and where should
> it be set in the header ?
The scale factor corresponds to (from dbh.h):
struct image_dimension /* image_dimension */
{ /* off + size*/
...
float funused1; /* 72 + 4 */
in the header, and the origin is an idiosyncratic use made by SPM
of the
struct data_history /* data_history */
{ /* off + size*/
...
char originator[10]; /* 105 + 10 */
field, using it as short integers rather than a char string.
The scale factor is usually set from the data in the images files from your
scanner, by conversion programs. We get CTI images from our reconstructions
and the scaling information in these images is written into the scale factor
in the analyze image.
Hope that helps,
Matthew Brett
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