> To be sure that there wasn't a problem with flip change, I copied the raw
> data into a new directory. Confirmed that defaults.analyze.flip was set at
> 0, and then redid the
>
> realignment/resplicing.  Same results:
> >> spm_defaults
> >> spm_orientations
>
> LAI   Left-handed  bold3_5.img
> RAI  Right-handed  rbold3_6.img
>
> My raw bold files have a .mat file associated with them.  If I copy just
> the .img and .hdr files to
>
> a /no_mat directory, and run spm_orientations:
> >> spm_defaults
> >> spm_orientations
>
> LPI  Right-handed  bold3_5.img
> In these no .mat file images the eyeballs face right in sagital view, down
> in axial. They retain these features LPI, right handed, eyeball direction
> after realignment.  A .mat file was created after realignment for the raw
> data images (before reslicing). But not for the first image.  Also, the
> realigned images do not have .mat files.  Based on your comments below, I
> take this to indicate that (1) there was sufficient information in the .hdr
> file so the first image didn't get a .mat file (is this correct, I wasn't
> entirely sure I got your info about this clear); (2) the origin field in
> the first image's .hdr is NOT [0 0 0])

It seems to be the case that the resliced images don't need .mat files.  As 
you can see, with flip=0, images without .mat files are assumed to be 
right-handed.  If flip remains at zero, then the handedness will be 
consistent throughout - although you may need to rotate the data via the 
Display button in order to get it to spatially normalise properly.

Alternatively, if the data had been copied without .mat files, and flip was 
set to 1 (permanently), then the data would be considered as being stored 
left-handed throughout.

I can't remember how your data are stored now though.

>
> O.K., I for some reason thought that I should check the voxel sizes by
> surfing around on the Display, rather than checking in the right hand box. 
> These data do have the x value negative for the raw images with a .mat
> file. After realignment, the x value is positive.  Presumably, this doesn't
> actually flip the data, though, right?

Whether or not there is a -ve voxel size indicates whether flipping takes 
place in order to view the coordinates within a volume in a right-handed 
system.  If the data are stored left-handed and viewed as right-handed, then 
there is a flip.


>  This subjects midline is angled a
> bit so it's possible to see if the brain was actually flipped (as in when I
> do -x) but the angle is the same for the raw and realigned images (although
> the raw have -x, y, z; and realigned have x, y, z for Voxel Size).

If you use the Check Reg button, then you should be able to see if one image 
appears flipped relative to another - from the pattern of sulci etc.


> O.K., so if the Display Voxel Size is:  -x, y, z and the eyeballs look up
> and to the left, does this tell me what the orientation is...?

If any voxel size is shown as negative, then you know that SPM thinks the data 
are saved as left-handed.


> NO DEFAULTS LOADED:
> >> spm_orientations
>
> LAI   Left-handed  bold3_6.img
> RAI  Right-handed  rbold3_5.img  (WARNING MESSAGE FOR RBOLD DELETED FOR
> EASE(!?) OF PRESENTATION) LPI  Right-handed  wrbold3_9.img Warning: Cant
> get default Analyze orientation - assuming flipped LPI  Right-handed 
> swrbold3_9.img

I'm not sure why images without .mat files are appearing with right-handed 
storage.  The only way I can think of is that running the 
spm_flip_analyze_images returns an answer of zero.


> To add to the confusion, I'm dealing with two data sets, one collected
> during Summer 1, the other during Summer 1, on different Sonata's (at the
> same location).  Unbeknownst to me, the defaults for flipping on the two
> were different.  I discovered this as I was processing the data, this is
> part of the process of my sorting out the specifics associated, in part,
> with those defaults.  The LAS image was from the Summer 1 data set, this
> entire email is about Summer 2 subjects.

When checking the handedness of original and resliced images, it is useful to 
check that of the first image in the series (i.e. the one that images are 
registered with - or resliced to match).  The handedness of resliced data is 
the same as that of this first image.

I'm getting a little confused with everything now.  I think the bottom line is 
that you should make sure you know the order in which the voxels of the 
images are stored before you begin.  If you run spm_orientations, then you 
should be able to confirm that everything is correct.

Once this is correct, and providing the flip never changes, all the realigned 
and spatially normalised data should remain in the correct handedness.

Note that if you reslice left-handed data (i.e. data that SPM assumes is 
stored left-handed) to match right-handed data, then the resliced files will 
be right-handed (i.e. the same as the reference image).  Is there any chance 
that you may be mixing data from one scanner with that of the other?

Does this help?

Best regards,
-John