Dear Denis, list,
all the batch engines I heard of, including our own, can be found on the extensions pages on the SPM2 website http://www.fil.ion.ucl.ac.uk/spm/
As you noticed, most of these engines are geared towards fMRI, but fMRI analysis does require quite some preprocessing, actually, involving coregistration, normalisation, etc. So I'd suggest you have a look at them and pick the one that is most convenient to you.
After the discussion last year we started to build our spm2-batch engine (as did some others), which is now available under:
http://spm2-batch.sourceforge.net/
Have a look at our source code to see how we did that, feel free to make additions for segmentation etc. Should be doable with some matlab knowledge. And don't forget to send me what you made ;-) I could include it in our engine. That is how it took shape in the first place, by contributions from various users both within our institute and from the list.
Good luck,
Bas
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Dr. S.F.W. Neggers
dept. of Psychonomics,Helmholtz Institute
Utrecht University
Heidelberglaan 2
3584 CS, Utrecht, room 17.09
the Netherlands
Tel: (+31) 30 253 4582 Fax: (+31) 30 2534511
E-mail: [log in to unmask]
Web: http://www.fss.uu.nl/psn/web/people/personal/neggers/
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-----Oorspronkelijk bericht-----
Van: SPM (Statistical Parametric Mapping)
[mailto:[log in to unmask]]Namens Denis Brown
Verzonden: woensdag 12 oktober 2005 16:14
Aan: [log in to unmask]
Onderwerp: [SPM] structural MRI and batching
Dear SPM gurus!
My group processes structural MRIs from an elderly subject population and
hence face the problems of atrophied brain images, etat crible, and so
on. We find a need to create our own templates for subpopulations and
generally I think do more processing than folks working with "normal"
populations. A desire to use batch processing, once the images have been
stripped, AC-PC aligned, etc is quite high on the agenda.
I note some discussions especially from September last year on this list
(Yanjun, Neggers, et al), where batch processing was often mentioned in the
context of fMRI. In a nutshell, what is the status of SPM's batch
capabilities as relates to structural work for normalisation, segmentation
and the production of templates?
It would be wonderful, for example, to be simply able to edit a list of
filenames to include or exclude subjects newly enroled to or deleted from a
study, or to create fresh file lists to automate the process of creating
different subpopulations within our overall cohort (eg. clinical symptoms
vs symptom-free.) The current pointy-clicky GUI interface manual method
is error prone at best. Using imcalc's parameter setup
(i1+i2+i3+...+iN)/N can also be error prone and rather tiresome to input
for large N.
Kind regards,
Denis
(Sorry for a possibly "dumb" question.)
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