Dear Christian,

I can understand your point ii) below on the slice timing correction. (Though see below the difference between my images/session and images/subject. Additionally, the estimation portion of the analysis also needs the whole time series for a voxel in memory but utilized the maxMem aspect of memory management, slice time correction could do the same).

But i) for motion correction I don't quite understand. As the motion correction is rigid body, and everything get's corrected to the first image (as reference), but does image 1000 (as an example) need to be in memory the same time as image 10, especially when it is in different session? 

I guess the issue is that when I ran two jobs in parallel that had small number of images (200/session) these ran fine. 

When I then setup a bigger job in which I have 6 sessions per subject, the whole 6 sessions worth of data need not be in memory all at once. Especially since these data are seperated in time by up to a few minutes. However, the behavior of spm99 is such that it does bring in 1200 images when really it should only bring in the 200 at a time. Certainly that could be fixed and this is what I am suggesting. 

I fully understand the nature of (free) research tools etc, nothing wrong with making suggestions. 

I apologize in advance if my "tone" has been taken too personal.

Sincerely,

Robert

>>> Christian Buechel <[log in to unmask]> 09/04/00 02:24 AM >>>
Dear Robert,


> What seems silly is that realignment  (also, smoothing, coregister, normalization) is a process that does NOT require all images to be in memory at once, since they are being realigned to the first common image. (Admittedly, slice timing does, but only a small handful for interpolation).

(i) if you motion correct the time-series during realignment the whole time-series needs to be processed.
(ii) in slice timing correction we chose Fourier interpolation to shift the phase and again the whole time-series needs to be in memory.

>  What would seem to be actually better programming practice would be to only hold in memory the image that is being realigned (smoothed, coregistered, normalized) Or, if there is sufficient memory, a small number of images optimized disk i/o.

The mails by R. Welsh prompt me to comment on a recent change in "tone" on the SPM helpline. SPM is a research tool provided free of charge by the methods group of the Wellcome Dept of Cognitive Neurology. Although I can understand that it is annoying when SPM crashes, it is inappropriate to
ask for fixes "ASAP" and imply that the code (and author?) "seems silly". Don't forget, the authors are scientists. Their main job is research. I am using SPM for 5 years now and find it a wonderful tool and toolbox. Nobody has to use it. Be assured that the authors address questions asap,
without explicitly being asked to.

--

-Christian Buechel

--
Dr. Christian Buechel
Neurologische Universitaetsklinik, Haus B
Universitaets-Krankenhaus Eppendorf
Martinistr. 52
D-20246 Hamburg
Germany
Tel.: +49-40-42803-4726
Fax.: +49-40-42803-5086
email:[log in to unmask]
www.uke.uni-hamburg.de/kliniken/neurologie/pages/mitarbeiter/buechel_c.htm
www.uke.uni-hamburg.de/kliniken/neurologie/pages/forschung/cnl_index.htm





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