Dear SPM users,
sorry to bother you again with the "hdr edit" topic.
*John Asburner wrote:
>It was removed as I consider it to be too dangerous. Too many people used
>it to change the origin or voxel sizes of their .hdr files, and wondered
why
>these appeared to remain the same (because of the .mat file). This is
>likely
>to cause even more problems with SPM2b, as the data are (for most people)
>implicitly flipped.
When the AC line is set at the origin in the HDR file as the first step in
preprocessing, i.e. when no .mat files have been created, no danger is
present.
In general, i thought that it should be wise to set the origin of all images
to obtain similar starting points for coreg-realign-normalize steps, whose
underlying minimilization-algorithms could otherwise get stuck in local
minima.
On the other hand, mathematically it is similar to obtain starting points
for preprocessing steps by means of a translation, which is saved in a .mat
file, and hence setting the AC point to the origin is not longer necessary.
It is kind of naieve to expect that everyone is knowing what he or she's
doing, and I understand the dangers of changing origins in the header file
when one doesnt know what is computationally going on.
So my main question is mainly a practical one: is there still the need to
alter the origin in the Analyze-header at the AC line in spm2b? Or can one
now roughly pre-register the images with a translation matrix and leave the
header file unchanged?
Thank you in advance,
Bas
--------------------------------------------
Dr. S.F.W. Neggers
dept. of Psychonomics,Helmholtz Institute
Utrecht University
Heidelberglaan 2
3584 CS, Utrecht, the Netherlands
Tel: (+31) 30 253 4582
Fax: (+31) 30 253 4511
E-mail: [log in to unmask]
Web: http://www.fss.uu.nl/psn/pionier
--------------------------------------------
-----Original Message-----
From: Kathryn Moores [mailto:[log in to unmask]]
Sent: dinsdag 17 december 2002 4:55
To: [log in to unmask]
Subject: Re: HDR edit in spm2b
Hi Zhang,
John Ashburner answered this question the other day. I have pasted his
response for your information.
Regards,
Kath
>> Regarding the HDR edit function - was it removed from this version of spm
>> (why)or is it hiding somewhere in the menus?
It was removed as I consider it to be too dangerous. Too many people used
it to change the origin or voxel sizes of their .hdr files, and wondered why
these appeared to remain the same (because of the .mat file). This is
likely
to cause even more problems with SPM2b, as the data are (for most people)
implicitly flipped. There are also a few other fields in the .hdr that are
now used in order to achieve slightly more compatibility with the true
Analyze
7.5 format. If you know what you are doing, then the easiest way to modify
the
header contents is probably by:
P = spm_get(1,'*.img');
V = spm_vol(P);
% Modify the fields you want to change.
Vo = spm_create_vol(V,'noopen');
If you really want a header editing utility, then I think Darren has one.
If
you want to see the full contents of an image header, then try:
hdr = spm_read_hdr(spm_get(1,'*.hdr','Select .hdr file'))
hdr.hk
hdr.dime
hdr.hist
Best regards,
-John
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On
Behalf Of Zhang Zhijun
Sent: Tuesday, 17 December 2002 1:40 PM
To: [log in to unmask]
Subject: HDR edit in spm2b
Dear all:
Is there HDR edit function in the spm2b version? I can't find it.
there is this function in spm99b, I think this function is useful, why
there is not this in spm2b? can anyone give me a hint?
regards,
zhang zhijun
|