I am also having some problems with the adapting the batch file given on
the mailing list.  I was able to patch the one listed below and a few
others, but I am pretty new to SPM and can't figure out the following
error:

??? Reference to non-existent field 'u'.

Error in ==> /opt/local/spm2b/spm_Volterra.m
On line 41  ==>     for k = 1:size(U(i).u,2)

Error in ==> /opt/local/spm2b/spm_fMRI_design.m
On line 280  ==>                [X,Xn,Fc] = spm_Volterra(U,bf,V);

Error in ==> /opt/local/spm2b/spm_fmri_spm_ui.m
On line 209  ==>        SPM       = spm_fMRI_design(SPM);

Error in ==>
/denali/data7/ubc_nc_ap3_spm2b/test/stats/duration_0/stats_batch.m
On line 51  ==> SPM = spm_fmri_spm_ui(SPM);

Obviously I haven't set this field, but I am not really sure how to set
it because from referencing some other SPM.mat files it looks like a
pretty complicated structure.  In SPM_fMRI_design it describes this
field as (t x j) inputs or stimulus function matrix.

Any help would be appreciated.

Kim

>>> Karl Friston <[log in to unmask]> 12/06/02 07:09AM >>>
Dear Thierry,

>I have been using SPM2b batch mode in the first-level analysis of an
>fMRI study.  It is truly clearer than the previous batch modes in
>SPM99:  it is straightforward to understand the meaning of (most of)
>the SPM.mat elements.  It might be useful to compile in a single
>explanatory file the meaning of each element in the matrix.
>However, adapting the batch file given on the mailing list in a multi
>session analysis I encountered a small problem:  there is no
>reference to the question "Are session replicated?" in the SPM.mat
>file (or none I could find).  I resolved this by  adding an element
>in the SPM.mat find (like SPM.repl= 0|1) and a "try/catch" loop in
>the spm_fMRI_design.m, line 222.  I don't know if this is necessary
>or  if there are other tricks but it worked perfectly.

Yes - we have come across this bug here.  We have modified
spm_fMRI_design from:

if length(SPM.nscan) > 1 & ~any(diff(SPM.nscan))

to

if length(SPM.nscan) > 1 & ~any(diff(SPM.nscan)) &
~isfield(SPM,'Sess')

In principle this should work.

>But I have an error in the second level analysis (first level is
>multi session/single subject).  After using "Basic models->One sample
>t-test", SPM2b writes an SPM.mat in the folder, but cannot estimate
>it (neither with "results" or "estimate").  It gives the error
>message given at the end of this mail.  I checked manually that
>SPM.mat doesn't have a reference to SPM.xVol (other elements are
>missing too).
>I think maybe the new SPM.mat features used in SPM2b wasn't updated
>in the "basic model" evaluation.  Anyway, any help on how to
>implement the second-level analysis with SPM2b will be greatly
>appreciated!

Only the fMRI routines are called by the batch script released on
this helpline.  PET and basic models call spm_spm_ui which has not
been 'batched' yet.  It is possible to call spm_spm_ui directly but
the design specification is not so transparent.  We left this out
because PET and second-level fMRI analyses are usually quite simple
and quick to do by hand.

If you cannot estimate a basic model (specified through the GUI)
could you let me know what error messages are returned by spm_spm
(this is the routine that fills in SPM.xVOL).

With best wishes,

Karl