Hi > On 3 Dec 2015, at 04:24, Bagrat Amirikian <amiri...@umn.edu> wrote: > Hi, > I have downloaded and unpacked HCP500_Parcellation_Timeseries_Netmats data. > My question is about group ICA spatial maps, specifically, about > melodic_IC.dscalar.nii and melodic_IC_ftb.dlabel.nii files in the groupICA* > subdirectories. There is a very short description of these files in the > accompanying PDF file: > > melodic_IC.dscalar.nii ICA spatial maps (unthresholded > Zstats); one "timepoint" per map. Grayordinates > melodic_IC_ftb.dlabel.nii Summary "find the biggest" labels image > for all ICA spatial maps. Grayordinates > > I have loaded these files generated for 25-dimensional group-ICA to wb_view > with corresponding Q1-Q6_R440_midthikness surface files for their inspection. > > 1. I can appreciate Zstats maps provided for each IC by > melodic_IC.dscalar.nii. How were exactly these Zstats computed? Are these > regular Z-scores obtained by subtracting the vertex/voxel-wise mean and > dividing by the standard deviation, or something else? > Not quite - these are "z-stats" as output by MELODIC ICA tool in FSL (see Beckmann IEEE TMI 2004). The simple answer is that the ICA maps are fed into a mixture model to normalise the central/null part of the distribution across voxels. > 2. When I click on the map and Information Window pops up, it shows two > SCALAR values for the selected vertex. For example: > > VERTEX CortexLeft: 28165 > ANATOMICAL XYZ: -6.28827, 59.2204, -0.919904 > CIFTI SCALARS melodic_IC.dscalar.nii: 0.935668 -0.20834 > > What do these two numbers 0.935668 and -0.20834 actually mean? I though there > should be just one number corresponding to the Zstat of the vertex. > I don't know - when I try this I only get a single number. Do you have multiple similarly-named images loaded maybe? > 3. It appears that melodic_IC_ftb.dlabel.nii provides a hard > non-overlapping parcellation and labels each parcel (which could consist of > several spatially separated regions) by a color. The number of parcels > corresponds to the ICA dimension, 25 in this case. How is this parcellation > obtained? How is the set of spatially continuous/diffusive maps of individual > ICs give rise to this parcellation with sharp non-overlapping borders and > without any gaps between the neighboring parcels?
"ftb" - "find the biggest" - at each grayordinate the index number of the ICA component map having the highest value there is used. Cheers, Steve. > > Thank you very much for your help. > > Bagrat > > Bagrat Amirikian, Ph.D. > Department of Neuroscience > University of Minnesota Medical School > > Brain Sciences Center > Minneapolis Veterans Affairs Health Care System > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
