 |
 |
Dear João, On Thu, 22 Sep 2011 15:26:25 -0400, Jonathan Peelle <[log in to unmask]> wrote: >Dear Jo�o, > >> I'm running a VBM analysis with SPM8 and VBM8 toolbox. >> >> I have a couple of questions: >> >> - Is it better to report the voxel-level or cluster-level p-values? > >It's not that one is "better"�they are telling you about different >levels of inference. For the voxel-level correction, it tells you >that every voxel you see is unlikely to have occurred by chance (and >thus, you could make some inference about that voxel). If cluster >level, it tells you that a particular cluster is bigger than you would >expect by chance. This entitles you to make some inference about the >cluster as a whole, but not subparts (which can get tricky if a large >cluster covers multiple regions of the brain). There are several >other emails in the archives that go into more detail. > > >> - If I use the "Results" button in SPM8, does it use the non-stationary >> cluster extent correction to calculate valid cluster p-values? Is the method >> of Satoru Hayasaka et al. 2004 implemented in SPM8 or should I use an >> external toolbox, like the NS extension by Hayasaka et al >> (http://fmri.wfubmc.edu/cms/NS-General) ? > >The "results" button in SPM does not correct for non-stationarity >which is present in VBM images. You'll need to use the ns toolbox. >Unfortunately, as far as I know the ns toolbox is not available for >SPM8 (nor will it be), which means using SPM5 for looking at your >results. As far as I'm aware this should not present a problem, as >the statistical machinery has not changed appreciably (but I would be >interested to hear if I'm wrong about that!). > There is an option for the newest SPM8 releases (>=4010), which enables non-stationarity correction on the cluster level. Please set in spm_defaults.m: defaults.stats.rft.nonstat = 1; However, this option will result in a much longer calculation if you print the results table. This is maybe also the reason that this option is not set as default. >I don't know whether the VBM8 toolbox includes anything for >non-stationarity correction�it would be worth checking. I have removed this option from the interface because of the interferences with the SPM interface. There is still a hidden option if you choose the option "Transform and threshold spmT-maps". Regards, Christian ____________________________________________________________________________ Christian Gaser, Ph.D. Departments of Psychiatry and Neurology Friedrich-Schiller-University of Jena Jahnstrasse 3, D-07743 Jena, Germany Tel: ++49-3641-934752 Fax: ++49-3641-934755 e-mail: [log in to unmask] http://dbm.neuro.uni-jena.de > > > >> - If I choose "none" for the "p value adjustment for control" it will aply >> the following threshold to each voxel, am I correct? But even if I choose >> "none" correction I still get the FWE-corrected cluster-level and I get >> FWE-corrected cluster-level p-values... why is this? > >You are correct�if you select "none", it will apply that threshold at >the voxel level. You can think of this as defining features >(clusters) in your data. You have not corrected for multiple >comparisons at the voxel level (because you selected "none"), but you >can still correct for multiple comparisons at the cluster level. >Having defined your clusters using some threshold, SPM will therefore >give you the corrected p values for each cluster. These are perfectly >valid, provided that (a) you understand the level of inference you're >working at (see above) and (b) in the case of VBM, you have accounted >for non-stationarity in the data. > >This previous message may also be of some help: > >https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;8b567b91.1107 > > >Hope this helps! > >Best regards, >Jonathan > > >-- >Dr. Jonathan Peelle >Department of Neurology >University of Pennsylvania >3 West Gates >3400 Spruce Street >Philadelphia, PA 19104 >USA >http://jonathanpeelle.net/