Hi > On 3 Dec 2015, at 20:27, Bagrat Amirikian <amiri...@umn.edu> wrote: > Thank you very much Steve for your prompt response! > > 1. I looked into Beckman IEEE TMI 2004. Is there any way to find out the > threshold ‘Z-stats’ for each IC corresponding to the 0.5 posterior > probability activation in the framework of Gaussian mixture model? In other > words, how to use the provided Z-stats distributions, how to find a > reasonable Z-stats threshold for an individual IC? Can such a threshold > selection procedure be automated, or one needs to go over all components > manually and after visual inspection make a selection?
If you run melodic with all output options turned on, you can find various things relating to the mixture-model fitting and related thresholding (for the web report images). However for these HCP group-ICA maps, no thresholding was applied (eg when using these as "parcellations" for generating the node timeseries. > > 2. I was running two instances of wb_view in Windows 7, the second one loaded > with WB_1.0_Tutorial. After closing them and then opening only one instance > of wb_view loaded with group-ICA, only a single number appeared. Should this > be reported as a bug in wb_view for Windows? Sorry I'm not a wb_view expert so would need someone else to comment on that. Cheers, Steve. > > 3. Thanks for the explanation. > > Cheers, > > Bagrat > > > From: Stephen Smith [mailto:st...@fmrib.ox.ac.uk > <mailto:st...@fmrib.ox.ac.uk>] > Sent: Thursday, December 03, 2015 2:43 AM > To: Bagrat Amirikian > Cc: hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] group-ICA spatial maps > > Hi > >> On 3 Dec 2015, at 04:24, Bagrat Amirikian <amiri...@umn.edu >> <mailto: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 <mailto: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/> --------------------------------------------------------------------------- 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
