Thank you for the info Dr. Glasser. Glad to know how melodic_IC_sum.nii.gz is generated. I think it might be helpful to put this info into the "HCP500_GroupICA+NodeTS+Netmats_Summary" document.
Best, Cherry On Tue, Mar 3, 2015 at 8:04 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: > A better way to put it is any volume-based group average cortical result > is not an accurate representation of the underlying subjects’ data. The > results that Mike was talking about are generated by taking the group CIFTI > ICA results and dual regressing them into each individual’s CIFTI dense > timeseries (for stage one of dual regression) and then the resulting > individual subject component timecourses into each subject’s volume > timeseries to make individual subject component spatial maps in the > volume. This is accurate as far as getting individual subject volume maps > (because we don’t apply any volume-based smoothing), however as soon as you > try to average these maps across subjects (to create melodic_IC_sum.nii.gz) > you aren’t aligning like with like any more and hence get an inaccurate > result. > > Peace, > > Matt. > > From: Yizhou Ma <maxxx...@umn.edu> > Date: Tuesday, March 3, 2015 at 7:15 PM > > To: Timothy Coalson <tsc...@mst.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] projecting from volume to R440 template > (subcortical and cerebellum) > > Hi Timothy, > > Thank you for your reply. So sounds like that the file Atlas_ROIs.2.nii.gz > for whichever subject can get me the same result? > > I'd also like to follow up on Dr. Harms' suggestion on using > melodic_IC_sum.nii.gz. Given the discussion on the inaccuracy in group > level surface/volume mapping, it seems that melodic_IC_sum.nii.gz is not an > accurate representation of the HCP maps in the MNI space, thus it is "for > reporting purposes"? > > Thanks, > Cherry > > On Tue, Mar 3, 2015 at 7:06 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> It isn't impossible to get the data into the grayordinate space we use, >> though the volume to surface mapping part could be problematic because of >> alignment/group average issues. As long as the data is nonlinearly >> registered to MNI152 space, you are really only missing the volume >> subcortical label file to be able to create a cifti file in our >> grayordinate space. I think you can get this file by downloading a single >> subject's dataset from connectomedb (download images, structural >> preprocessed?). >> >> There will be an enhancement added to wb_command that will allow you to >> create this volume label file from an existing cifti file, rather than >> downloading it. >> >> Tim >> >> >> On Mon, Mar 2, 2015 at 2:13 PM, Yizhou Ma <maxxx...@umn.edu> wrote: >> >>> Thank you for your suggestion Dr. Harms. It seems that it is the only >>> way to compare subcortical networks at this moment. >>> >>> On Mon, Mar 2, 2015 at 12:21 PM, Harms, Michael <mha...@wustl.edu> >>> wrote: >>> >>>> >>>> Not sure if this will help your purposes, but the >>>> "HCP500-PTN" (Parcellation+Timeseries+Netmats) distribution includes the >>>> following: >>>> >>>> melodic_IC_sum.nii.gz: ICA spatial maps projected from the surface >>>> into the volume, for reporting purposes. MNI152 space. >>>> >>>> I don't think we have any group ICA maps derived originally in the >>>> volume space since the group ICA was done using the FIX-cleaned CIFTI time >>>> series as inputs. >>>> >>>> cheers, >>>> -MH >>>> >>>> -- >>>> Michael Harms, Ph.D. >>>> ----------------------------------------------------------- >>>> Conte Center for the Neuroscience of Mental Disorders >>>> Washington University School of Medicine >>>> Department of Psychiatry, Box 8134 >>>> 660 South Euclid Ave. Tel: 314-747-6173 >>>> St. Louis, MO 63110 Email: mha...@wustl.edu >>>> >>>> From: Yizhou Ma <maxxx...@umn.edu> >>>> Date: Sunday, March 1, 2015 10:23 PM >>>> To: Matt Glasser <glass...@wusm.wustl.edu> >>>> >>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> Subject: Re: [HCP-Users] projecting from volume to R440 template >>>> (subcortical and cerebellum) >>>> >>>> Thank you for your reply Dr. Glasser. I've read this recommendation >>>> elsewhere on the forum and your point is well taken. Yet in our case the >>>> purpose is a bit different. We are not trying to do any analysis but to >>>> compare the HCP ICA maps with classical maps that have been generated in >>>> the volumetric space. Although this may not be accurate, it'll offer us >>>> some insight into the HCP maps. >>>> >>>> On Sun, Mar 1, 2015 at 10:09 PM, Glasser, Matthew < >>>> glass...@wusm.wustl.edu> wrote: >>>> >>>>> I would recommend mapping your individual subject data onto >>>>> individual subject surfaces and then registering on the surface. Volume >>>>> to >>>>> surface mapping onto a group average surface from a group average volume >>>>> is >>>>> not particularly accurate in comparison. Once you average cortical data >>>>> in >>>>> the volume, you lose the ability to do accurate spatial localization to >>>>> cortical areas. Instead data can be easily mapped onto locations >>>>> centimeters away in 2D from the correct location on the folded cortical >>>>> sheet. Also, group average surfaces are very blurry in many cortical >>>>> regions because different people have different folding patterns that >>>>> cannot be registered (e.g. some people can have two gyri where others have >>>>> only one). Thus, it’s really better to do your cortical analysis on the >>>>> surface to begin with, as we do in the HCP with CIFTI. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: Yizhou Ma <maxxx...@umn.edu> >>>>> Date: Sunday, March 1, 2015 at 9:27 PM >>>>> To: Timothy Coalson <tsc...@mst.edu> >>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>> Subject: Re: [HCP-Users] projecting from volume to R440 template >>>>> (subcortical and cerebellum) >>>>> >>>>> Hi, >>>>> >>>>> I am still looking forward to getting help on this issue. Is an " >>>>> Atlas_ROIs.2.nii.gz" or similar files provided for volume to surface >>>>> mapping onto R440 group template? If not, will there be any in the future? >>>>> >>>>> Thanks, >>>>> Cherry >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> HCP-Users@humanconnectome.org >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> The materials in this message are private and may contain Protected >>>>> Healthcare Information or other information of a sensitive nature. If you >>>>> are not the intended recipient, be advised that any unauthorized use, >>>>> disclosure, copying or the taking of any action in reliance on the >>>>> contents >>>>> of this information is strictly prohibited. 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