On Wed, Aug 2, 2017 at 6:02 PM, James Morrow <james.mor...@monash.edu> wrote:
> Thanks Tim and Matt for the detailed responses. > > > I agree that mapping to volumes is sub-optimal. Our goal is to identify > coords to be used as targets for brain stimulation with TMS. We need MNI > coords for neuronavigation. Given the extent of the TMS field, we have some > tolerance for imprecisions in the mapping. > I see. We generally get asked these questions in the context of fMRI analysis, hence our reluctance. How does the neuronavigation go from MNI coordinates to subject coordinates, do you happen to have a reasonable T1w MRI scan of your subjects? I don't know how big the TMS field is, and I hadn't looked at the distance from subject to group average surfaces before, but in one of the HCP subjects, I got a maximum of 2cm distance from the group average surface (using midthickness surfaces), which occurred in a few specific locations, while 90% of the surface was 1cm distance or less. > Can I clarify – was the ICA run on the volumes and then later mapped on to > surfaces, or was it performed on the surface data? If the former, are the > original volumetric results for the ICA of each subject available anywhere > in .nii format? > > > Cheers, > > James > > *James Morrow* > Research assistant > Brain & Mental Health Laboratory > > *Monash Institute of Cognitive and Clinical Neurosciences* > School of Psychological Sciences > Monash University > c/o MBI, 770 Blackburn Road > Clayton VIC 3800 > Australia > > T: 03 9902 9768 > E: james.mor...@monash.edu <amy.al...@monash.edu> > www.med.monash.edu.au/psych/bmh/ > > <http://www.med.monash.edu.au/psych/bmh/> > <http://www.monash.edu/neuro-institute/> > > On 3 August 2017 at 07:00, Timothy Coalson <tsc...@mst.edu> wrote: > >> As Matt said, "MNI coordinates" of functionally-aligned cortical surface >> features don't have much meaning, similar to how T1w-aligned MNI space >> volumes don't have good cortical functional alignment (except in a few >> low-variability regions). We have shown that group average surface >> coordinates do not follow the MNI cortical ribbon (see attached image that >> simply shows the average white and pial contours on top of the MNI >> nonlinear template). The ICA maps themselves are also more informative >> than just the vertices at their peaks. >> >> Surface group results should not be turned into volumetric files, group >> average surfaces do not have much folding left in them, and as such they do >> not match the MNI template anymore - this is due to folding >> incompatibilities between subjects, but also due to using functional >> surface registration instead of folding patterns. Using the individual >> surfaces to map to the volume and then averaging across them would spread >> your data out just as badly as doing volume-based analysis of cortex, so >> this is also highly discouraged. >> >> Despite strongly advising you not to do what you outlined, I will tell >> you what commands you would need. The -cifti-extrema command will output a >> map with 1s and -1s at each local extrema. The surface it uses is for >> neighbor information and distance computation - this isn't as critical as >> coordinates are, as it merely sets the maximum possible density of extrema >> (what you could get from a very noisy map). You will need to use a >> threshold or other method to exclude local extrema that are outside the >> high-valued area. We use midthickness surfaces for this kind of thing (and >> when doing some important spatial operation, we use corrected vertex areas >> to compensate for the loss of folding in group average surfaces, see >> -metric-smoothing). >> >> You can extract the coordinates of a surface file with >> -surface-coordinates-to-metric, and you can use -cifti-separate on the >> -cifti-extrema result to get those as metric files, so that the indices >> will match, so that you can use them in matlab or some other tool for >> ad-hoc analysis (alternatively, use -cifti-create-dense-from-template to >> put the surface coordinates into a cifti file). Since we advise not to do >> this with any group data, you are on your own here (finding the coordinates >> in a bunch of individuals and averaging those will give exactly the same >> bad answer, reflecting the fact that many/most functional areas have >> notably different MNI coordinates in each individual). >> >> Tim >> >> >> On Tue, Aug 1, 2017 at 7:46 PM, James Morrow <james.mor...@monash.edu> >> wrote: >> >>> Hi, >>> >>> >>> We have recently downloaded the HCP900 Parcellation + Timeseries + >>> Netmats (820 Subjects) dataset. >>> >>> >>> >>> We would like to obtain the MNI coordinates of cluster peaks in the >>> melodic_IC.dscalar.nii ICA maps. >>> >>> >>> >>> Is there any way to do this? >>> >>> >>> >>> Is the –cifti-extrema function of wb_command the correct command? It >>> requires a surface file, but I’m not sure which would be most appropriate >>> for the group ICA results. >>> >>> >>> >>> Alternatively, would there be a way to convert the dscalar file into a >>> standard volumetric nii so that I can use standard FSL tools? >>> >>> >>> Thanks >>> >>> >>> James Morrow >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
