Dear Darren,

> > (1) what do they mean by "unflip" or "flip" images? in other words,
> > flip =
> radiologist view or neurologist view?
>
>
> default is RAS (neurologist):
>
> right    +X
> anterior +Y
> superior +Z
>
[snip]

thanks for the information. I had been looking at it long and hard but
could not figure it out. I had to admit I did not bother to try the Analyze
Program, which we do license over here. ;(


>
> >
> > (2) The paragraph before it define what individual
> > char stands for in hist.orient begins with the line:
> >
> > "The data_history substructure is **not** required, ..." (emphasis mine)
> >
> > My 2p worth says that Analyze Header can be either 108 bytes long
> > (without hist substructure) or 348bytes long (with hist substructure).
> > I believe my interpetation is correct because the first field in
> > header_key is size_of_hdr, indicating analyze header can be of variable
> > sizes.
>
>
> Yes, possibly, but many programs demand that size_of_hdr is 348 or they
> complain and/or crash. So, I guess the hist substruct is required, in
> this sense.

I agree. I highlight this point to support your argument that one cannot
"assume" that hist.orient is correct by pointing out that this field might
not be available at all.

Moreover, the analyse format interpretation program we developed here try
to conform with published infomration on the format. We practise strict
adherance to publish information. This means it cannot crash/complain since
either format is valid. In my case, I have to deal with missing information
of course but that was our choice and I cannot complain.

>
>
> >
> > I agree. The problem with Analyze 7.5 format is that it is so commonly
> > abused. I think by making the 4th dimension = 1, SPM actually
> > misinterpreted the format (oh no, ... I am inviting a flame war here).
>
> I'm not sure what you mean here. I think the dim(4) is how many volumes
> in a time series.
> For an anatomical volume, it should be 1. Is this not
> the documented format? In any case, it makes sense to use it that way. As
> discussed in another thread, we can use pixdim(4) to store the TR.
>

Yes. I agree the fourth dimension can be is TR as we cannot find any more
dimension which agrees with pix_dim_unit (or something like it) = "mm" say.
However, I find it slightly difficult to decide whether TR should be stored
as second or miliseconds. These are ambiguities that I don't like about the
format.

I can see why people says a 3D file is a 4D files by setting pix_dim[4] to
1 in order to harness pix_dim[4] for storing TR. IMHO, this is a mistake as
it implies this file can, by itself, properly represents the whole
time-series.


[Aside] As we all know, SPM's spm_hread will disregards the 4th dimension
but spm_hwrite will write to 4D file with 4th Dimension = 1. I sometimes
exploit the fact that SPM will only read in the first 3D volume to display
the first volume without resorting to 4D->3D conversion first. It is useful
especially when I only want to see whether I have a "brain" or not. I
thought I share this will those who did not know about this "hack".


> > Also, although the examples do seems to indicate fields not filled in
> > have to be set to zero, since there is no sentence saying that this had
> > to be done, most people just leave the computer to it, resulting in
> > random
> values
> > in them. Moreover, hist.orient does not have an "unknown" field,
> > making it difficult to determine whether the orientation field is
> > properly filled or not.
>
> True. I have found that if it is empty, that is near enough to 'unknown'
> and I treat that as equivalent to the default RAS, with a warning that
> this is assumed.

Agreed. Luckily the unstated assumption for any 'unknown' in general is 0
and that '0' is undefined by design for hist.orient.
>
> > I do not seems to be able to access the website. Can you reconfirm the
> URL??
>
>
> try http://sourceforge.net/projects/eeg/ - look for the mri_toolbox
> download or
> http://sourceforge.net/project/showfiles.php?group_id=50847&release_id=11832
> 5 and look for the highlighted download
>
Thanks, at least the first one works fine.


Thank you for taking the time to answer my question.

Best regards,
Cinly