| T O P I C R E V I E W |
| melissa.slavin |
Posted - Jun 23 2004 : 2:56:23 PM
Hi All,
just trying to gauge whether there is enough interest to start an SPM group where we can meet maybe once every 2 weeks to discuss issues. I know there is a big range of expertise around BIAC and affiliates, but I'm sure we can all learn something from each other. This could be for people who do either pre-processing and/or the actual processing of data in SPM.
Please email me directly, and I'll post again once I work out whether it has enough interest.
thanks,
Melissa |
| 5 L A T E S T R E P L I E S (Newest First) |
| petty |
Posted - Jun 24 2004 : 3:07:23 PM
i've never had any problems using the golgi SPM99 pre-processing, then doing analyses through SPM2. The only problem i've encountered was that if you do your analyses/contrasts on golgi, you also have to use golgi to display them. It will not work to do everything on Golgi, then display them on windows through SPM. However, you can still display them through showsrs2 flawlessly. |
| melissa.slavin |
Posted - Jun 24 2004 : 3:01:46 PM
Hmmm...I thought we'd tried to go from SPM99 to SPM2 without success. Maybe it was after the contrast image stage. Anyway, the SPM website lists improvements made for SPM2, and this will be a far better explanation than me trying to bumble through something I only peripherally understand - http://www.fil.ion.ucl.ac.uk/spm/spm2.html
Melissa |
| gregory.mccarthy |
Posted - Jun 24 2004 : 2:52:40 PM
I would be interested to know how SPM2 differs from SPM99 in terms of the algorithms used for the pre-processing steps mentioned in my prior post. It is common for folks here to use the SPM99 pre-processing functions as called by the bputil pipeline, but then use SPM2 to compute their GLM and contrasts. That is, there is no requirement to use SPM2 for pre-processing in order to use SPM2 for model testing. However, is there an advantage for using SPM2 functions for pre-processing other than interface improvements or convenience?
-- Greg McCarthy |
| melissa.slavin |
Posted - Jun 24 2004 : 12:05:23 PM
Thanks Greg - good advice. I know Jimmy has done a great job putting batch scripts up for SPM99 pre-processing. If you want to do SPM2 analyses, however, you have to do the pre-processing in SPM2. There are batch scripts out there for SPM2 pre-processing as well (see for example Matthew Brett's webpage http://www.mrc-cbu.cam.ac.uk/Imaging/Common/spm2_batch.shtml). I personally am still struggling with doing processing on golgi using SPM2, so that is something we can perhaps discuss if we get the group up and running.
Melissa |
| gregory.mccarthy |
Posted - Jun 24 2004 : 11:51:17 AM
Melissa -
Those interested in SPM pre-processing should become familiar with the automated scripts that run on the P670 and do time-slice adjustment, motion correction, coregistration, normalization, and smoothing. All of these functions are carried out using SPM functions. Interested individuals should consult the posts by Jimmy Dias that discuss the bputil pipeline.
-- Greg McCarthy
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