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Dear Miss Engineering, I'm afraid you cannot use that option unless your input data is a 4D image (lots of 3D volumes) which represent the results of statistics on appropriately permuted data. It is essentially a very low-level randomise-like functionality (where randomise is our tool for permutation-based non-parametric statistics). If you only have a 3D image containing one z-value at each voxel then this is not an appropriate option to use. If all you have are z-values then you can only convert them to the equivalent p-values. Whether the p-values are corrected or uncorrected depends on how the z-values were created. If they came from a FEAT analysis then they are uncorrected and you can only use fslmaths to get uncorrected p-values. All the best, Mark On 16 Sep 2011, at 17:13, Leslie Engineering wrote: > Just to clarify, to use my zstat file from group analysis to get corrected p value map, could I used a command like: > > fslmaths zstat1.nii.gz -ztop -cpval pstat_image.nii.gz > > > > On Fri, Sep 16, 2011 at 12:03 PM, Leslie Engineering <[log in to unmask]> wrote: > Thanks! > > > On Fri, Sep 16, 2011 at 11:57 AM, Mark Jenkinson <[log in to unmask]> wrote: > Hi, > > Actually, even this minimal documentation is unfortunately misleading/erroneous. > As the name suggests, you should pass in a z-value and get out a p-value. > The "<p>" in the usage should really be a "<z>". > > $ ztop 1.65 > 0.049471 > $ ztop 2.3 > 0.010724 > $ ztop 3.1 > 0.000968 > > Jesper's suggestion, of using the fslmaths option, is more appropriate > for images containing z values. So choose whatever is most appropriate. > > All the best, > Mark > > > On 16 Sep 2011, at 16:52, David Flitney wrote: > >> The tool (part of FSL) is documented as follows: >> >> 1 $ ztop >> Usage: ztop <p> [-2] >> -2 : use 2-tailed conversion (default is 1-tailed) >> >> 2 $ ztop 0.9 >> 0.184060 >> 3 $ ztop 0.9 -2 >> 0.368120 >> >> On 16 Sep 2011, at 16:48, Leslie Engineering wrote: >> >>> I can't seem to find anything in the literature about ztop. Could you help direct me? >>> >>> >>> On Fri, Sep 16, 2011 at 11:24 AM, David Flitney <[log in to unmask]> wrote: >>> Don't know how to use fslmaths but single z-scores can be converted with ztop >>> >>> -- >>> Dave Flitney >>> IT Manager, FMRIB Centre >>> >>> On 16 Sep 2011, at 16:20, Leslie Engineering <[log in to unmask]> wrote: >>> >>> > How do I use fslmaths to do a statistical conversion from z value to p-value? >>> > >>> > THANKS! >>> >> >> -- >> Dave Flitney, IT Manager >> Oxford Centre for Functional MRI of the Brain >> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717 >> URL: http://www.fmrib.ox.ac.uk/~flitney >> >> >> > > >