Hi Linda,

I am sorry to hear that you are stuck using software that
only reads ANALYZE data...

There may be a few things to note:

1. Since 3dAFNItoANALYZE does not modify the data at all
(except possibly to reorient it (via -orient)), if it starts
in tlrc space, then it is still in tlrc space. There are no
transformations applied.

2. Part of the trouble with ANALYZE is that you do not know
the space of the data. So if you go: AFNI -> ANALYZE -> AFNI
(even via 3dinfo, say), then it may show that the space is
+orig, even if it should be +tlrc. That is okay. That is
life in ANALYZE format.

3. Also, ANALYZE does not store the orientation. So you
cannot tell what inferior or anterior without guessing from
the data. Importantly, how does one tell left from right?


Because of point #3, you need to be careful when converting
to ANALYZE, in that it is necessary to know the desired
orientation ahead of time. That is typically either LPI or
RPI. Of course, even with those 2 choices, one does not
know left from right.

So consider verifying with the software writers or help,
what the data orientation should be. If it should be RPI
for example, then use:

3dAFNItoANALYZE -orient RPI ANALYZE_DSET AFNI_DSET+tlrc

(where you decide on the 'AFNI_DSET' and 'ANALYE_DSET'
names).

Note that AFNI_ANALYZE_VIEW applies when reading back that
ANALYZE dataset.

- rick