Hi Ellen,

Thanks for uploading the data. Since this has gotten long,
let me first say that there are indeed 6 runs here, and that
there is no problem with Imon. But there is data from what
would be considered three scanning sessions, and Imon deals
with only one at a time.

--

I'm not sure about all of the keystrokes while sitting at the
scanner, but when you set your protocol and start scanning, a
new set of directories will be created as needed. Let us say
that directory 002 is created, and new I-files begin to be
placed there.

This will continue into 022 and 042, etc., until the run is
over. When you being the next run, the new files will go into
directory 042, then 062, and so on.

However, what appears to have happened is that it wasn't just
a new run that was started. Maybe the same protocol was
selected or something. When that happens, the scanner will
start a new set of directories, say 003, and continue into
023, 043, 063, etc.

So in your case, you have directories ending in 3, 4 5 and
6. In the 003 directory (or ??3 directories), there is only
one run. In the ??4 directories, there are 2 runs (though
it seems the beginning of the run is not present, note that
directory 004 was not part of the data, it started at 024).
And in directories ??5 there are 3 more runs. Directory
006 holds an anatomical scan.

So you do have 6 runs here (if you have directory 004), but
they are just considered three scanning sessions. Imon can
only deal with one scanning session at a time (that was the
design). So you will have to run it 3 times:

Imon -start_dir 003 -GERT_Reco2 -quit
Imon -start_dir 004 -GERT_Reco2 -quit
Imon -start_dir 005 -GERT_Reco2 -quit

After each command, you can run (or rename) the GERT_Reco2
script. But then you may need to rename the datasets to
reflect the correct run numbers, since they are no longer
sequential.

Hopfully run 1 is from 003, runs 2 and 3 are from 004, and
runs 4-6 are from 005. Then you can rename 3 005 runs as
follows, for example:

3drename OutBrick_r1+orig new_r4
3drename OutBrick_r2+orig new_r5
3drename OutBrick_r3+orig new_r6

And similarly for the 2 004 runs.

Is that reasonably clear?

- rick