> Date: Thu, 21 May 2015 20:01:55 +0100
> From: [log in to unmask]
> To: [log in to unmask]
> CC: [log in to unmask]
> Subject: Re: [SPM] VBM12, SnPM Nonstationary cluster issues
>
> Dear Erdem,
>
> There is now an option in SPM12's batch to compute total tissue volumes
> from segmentation results:
> SPM > Util > Tissue Volumes.
>
> Best regards,
> Guillaume.
>
>
> On 21/05/15 16:18, H. Nebl wrote:
> > Dear Erdem,
> >
> > See below for additional comments.
> >
> > 1) I don't think there has been any change for the non-stationary cluster correction between e.g. SPM12 and SPM8. If you want to use this correction you do not have to set up any new models, and there's no need to turn to SnPM, it's just modifying spm_defaults and loading the already estimated models via "Results", the results tables will reflect non-stat. corrected cluster p values then (which is not explicitely stated within the table though). Non-stat. cluster correction is usually considered a very good idea for VBM.
> >
> > 2) SnPM13 should be compatible with SPM12 (at least it was with the beta version SPM12b) and can be obtained via registering at http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/software/snpm/snpmreg .
> >
> > 3) There's no need to calculate anything manually if you go with the implemented correction, see 1)
> >
> > 4) No, just go with the correction.
> >
> > 5) When going with SnPM VBM data could be treated like an fMRI data set, instead of beta/con images from single-subject level you would select the s(m)wc1 files. Likely there are a few aspects that need some adjustments like masking, covariates (e.g. TIV) according to specific needs of VBM analyses, but the SnPM GUI should be similar to that within SPM.
> >
> > 6) This MarsBaR version http://sourceforge.net/projects/marsbar/files/marsbar/0.44/ should be compatible with SPM12. You can indeed use MarsBaR to extract GM values from a second-level VBM model, similar to extracting (cluster-averaged) beta/con estimates from a second-level fMRI model. There should be no difference in methodology between different toolboxes / scripts, it's really just computing the average across voxels. Of course some of them might be easier to handle, e.g. MarsBaR has a GUI, whereas get_totals.m is a simple m file without any further requirements (see http://www.nemotos.net/?p=292 for instructions). Just make sure that the dimensions and voxel resolution of the ROI mask files match those of the s(m)wc1 files, and check what the extracted values mean (with MarsBaR you get the average, if you want to convert it into volume [mm^3] you have to multiply by number of voxels and voxel size in mm^3).
> >
> >> any additional comments
> > I wouldn't use the term "VBM12" (which the subject implies) except you really rely on the preliminary VBM12 version. If you did not, then your preprocessing is based on the improved unified segmentation algorithm with 6 tissue probability maps ("Segment"), the "old" unified segmentation algorithm with 3 tissue probability maps ("Old Segment"), or the SPM12-compatible version of the VBM8 toolbox. You should make sure about that in a paper as the algorithms differ.
> >
> > Best
> >
> > Helmut
> >
>
> --
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG