-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi Ged,
yes, I'm pedantic about the format specification, but not about the
neuroimaging purposes behind the -ve pixdim values. The MNI template
brain volumes are essential. They had to be in neurological orientation
(T&T coordinates are neurological, I think), but the Analyze 7.5 format
is incompatible with neurological orientation. That is the beginning of
a saga we best not reiterate. I prefer and recommend never using
Analyze 7.5 files (or anything that pretends to be Analyze 7.5 files),
if you want to do any image manipulations in neurological orientation.
I think it is fine to "view" the data that is in an Analyze 7.5 file in
neurological orientation, but it is never a good idea to mess with the
orientation information in the data files on disk. There is no
documented standard format for doing that and, if there were, it would
not be an Analyze 7.5 format specification. Show me an Analyze 7.5
format specification with all the details on how to work with -ve pixdim
values, in a standardized way, and I will swallow every word. In my
mind, NIFTI is that solution. It's an adaptation of Analyze 7.5, but
let's not call it Analyze ;-) That's my preference and I feel safe in
that little cocoon, but thanks for the prod ;-)
Best, Darren
Ged Ridgway wrote:
> Hi Darren,
>
> I agree with your warnings, and your suggestion to use NIfTI if at all
> possible, but I think this is a little too strongly worded:
>
>> Your violating the Analyze 7.5 format specification, which does
>> not define -ve pixdim values. If any third-party software uses those
>> data files with -ve pixdim values, almost anything could happen to your
>> data.
>
> avwhd $FSLDIR/etc/standard/avg152T1 | grep pixdim
>
> reports a negative pixdim (pixdim1 = -2), and while it may be
> non-standard in terms of Analyze *specifications*, it is rather common,
> perhaps to the point of being "standard" in *practical* terms?
>
> Anyway, I guess the short answer is once again "use NIfTI" ;-)
>
> Best,
> Ged.
>
- --
Darren L. Weber, Ph.D.
Postdoctoral Scholar
Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.
Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber
pgp: http://dnl.ucsf.edu/users/dweber/dweber_pgp.html
"To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself."
Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.3 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
iD8DBQFF5d0KxaCYN7qs0v4RAv+gAJ0btwJY0TX8qfasSxx4HETrjOFTUgCdElrP
wS9MtC85+fkKxQiARGccJgs=
=d9TR
-----END PGP SIGNATURE-----
|