Hi - that would be one way to do it - but slices_summary is simpler than that - it just thresholds the zstats at Z>6
Cheers On 15 Sep 2014, at 07:26, Bryan Paton <[email protected]> wrote: > Hi Steve, > >> That's correct: the 3D NIFTI ICA maps are released "primarily for >> display purposes" - as you say, the cortical parts of these live on the >> cortical surface and are projected onto the 3D volumes - meaning indeed >> tha the volumes aren't "filled out" volumetrically. So when viewed on >> the surface, using the original CIFTI representation of these maps, they >> are contiguous and unthresholded. >> >> The maps as seen in the 3D NIFTI volumes supplied are also >> unthresholded, but the thumbnail PNG snapshots of these are indeed >> thresholded by slices_summary, to make viewing clearer. > > Thanks that does all make sense and sorry that this is essentially an FSL > question but... for completeness the thresholding is a result of voxels/nodes > exceeding the 0.5 (activation/background) threshold level after the mixture > modelling? > > Thanks. > > Bryan. > > >> >> Hope that makes sense, >> Cheers, Steve. >> >> >> >> On 15 Sep 2014, at 01:41, Bryan Paton <[email protected] >> <mailto:[email protected]>> wrote: >> >>> Hi HCP people, >>> >>> In the group-ICA results (the ICA parcellations), there is a volumetric >>> MN152 3D version of the ICA maps released as a Nifti file >>> (melodic_IC_sum.nii). Each of the volumes/series in the Nifti file >>> corresponds to a separate ICA map. When looking at the different >>> volumes/series in the Nifti file (which are really just the 3D >>> projections of the surface or cortical ribbon) you can see that many >>> areas of the surface have non-zero values. The example PNG files showing >>> the ICA maps projected onto an axial slice are a very handy summary but >>> they show much more discrete ICA activity compared to the raw Nifti >>> images. Were the ICA maps thresholded in some fashion in order to >>> generate the summary PNG files? What threshold (if any) was applied? >>> >>> Thanks. >>> >>> Bryan. >>> >>> -- >>> Bryan Paton, PhD >>> >>> 770 Blackburn Rd >>> Building 220, Rm 141 >>> Monash University >>> Clayton, VIC, 3168 >>> Australia >>> >>> +613 990 29790 >>> >>> Research Fellow, School of Psychological Sciences >>> EEG Lab Manager >>> EEG & fMRI, TMS, TMS & EEG Liaison >>> Monash Biomedical Imaging >>> 770 Blackburn Rd, Clayton VIC >>> >>> http://sites.google.com/site/bryanpaton >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [email protected] <mailto:[email protected]> >> http://www.fmrib.ox.ac.uk/~steve >> --------------------------------------------------------------------------- >> >> Stop the cultural destruction of Tibet <http://smithinks.net> >> >> >> >> > > -- > Bryan Paton, PhD > > 770 Blackburn Rd > Building 220, Rm 141 > Monash University > Clayton, VIC, 3168 > Australia > > +613 990 29790 > > Research Fellow, School of Psychological Sciences > EEG Lab Manager > EEG & fMRI, TMS, TMS & EEG Liaison > Monash Biomedical Imaging > 770 Blackburn Rd, Clayton VIC > > http://sites.google.com/site/bryanpaton --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected] http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
