Hello SPMers.
I am a relative novice with the following questions:
We have been using SPM2b but have now added SPM2 with subfolders to the
Matlab path (both in folder H and in folder M).
(We have not added it at the home directory level because we have data
that was done in SPM99 that we are still looking at.)
Our SPM2 has 3 subfolders (apriori, canonical, rend). I was not prompted
about a new pathdef.m file.
I have such a file in the folder and ls -l shows me, by the new date,
that it has been updated.
I have no problem reviewing Results (obtaining glass brain and volume)
for models that were run previously in SPM2b.
However, I am encountering two separate problems with NEW analyses in
SPM2.
I should say that all preprocessing was done in SPM2b, so as a
precaution, my first question is: Are such scans compatible with SPM2?
If not, are there any "fixes" or do we need to re-process the scans?
First problem:
In folder H:
I tried to run a model (by hand) with 8 conditions. The TR is 3.24. One
session with 312 scans.
When the graphic for the hrf function appears, the x-axis is 1000+ and
therefore the function is a pencil line up the y-axis. When the design
matrix appears, conditions 5-8 look fine (These contain scan bars for
every trial, as they are modelout conditions.) However, conditions 1-4
(the conditions of interest) show no scan bars at all.
(I had entered my variable vectors at the matlab prompt by typing the
name of the .m file that contains them. This is probably not the
problem, as the modelout conditions were read successfully.)
Second problem:
In folder M:
I tried to run a model (by hand) that has 14 conditions, TR is 4.1.
There are 540 scans. These scans were acquired in 3 sessions (180 x 3)
but we concatenated the sessions (in the matlab vectors, not in the
fscans folder) because one session has no trials of one of the
conditions.
I had followed the "fMRI Design" prompts and then the "fMRI Data"
prompts, including selection of all scans for the 3 sessions.
Although I get a narrow hrf function on the graphic (x-axis is 600+),
the design matrix looks normal.
However, when I click on "Estimate" I get a pop-up error message:
"Please assign data to this design. Use fMRI under model
specification."
In the command window, the message said "Warning: One or more arguments
not
assigned during call to 'spm_spm' "
I looked in the root directory and there is no spm_spm.m in spm/spm2 or
its subfolders.
Next down on the path after spm2 is spm2b. spm2b does have spm_spm.m
The lines proceed as follows within that file:
function [SPM] = spm_spm(SPM)
SCCSid = '2.58';
SPMid = spm('FnBanner',mfilename,SCCSid);
Finter = spm('FigName','Stats: estimation...'); spm('Pointer','Watch')
try
SPM.xY.VY;
catch
helpdlg({ 'Please assign data to this design',...
'Use fMRI under model specification'});
spm('FigName','Stats: done',Finter); spm('Pointer','Arrow')
return
end
So the problem seems to do with try SPM.xY.VY;
The comment for that is:
% required fields of SPM:
%
% xY.VY - nScan x 1 struct array of mapped image volumes
% Images must have the same orientation, voxel size and data
type
% - Any scaling should have already been applied via the image
handle
% scalefactors.
%
(Note: For this model, I had typed spm_defaults at the matlab prompt (UK
defaults) to avoid an error message "Warning: Can't get default analyze
orientation -- assuming flipped". ) I encounter the defined problem with
or without this procedure.
Your help would be appreciated.
Thanks.
Regards,
Kathleen Smith
Toronto Canada
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