Ah great. I could not find much of any documentation (online) for slices_summary, merely that it takes an input 4D series, a threshold, a background image and the output directory.
Thanks again. Bryan. On 15/09/2014 4:24 PM, Stephen Smith wrote: > 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] > <mailto:[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]> >>> <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]> >>> <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] <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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
