Well, if they want to get to cifti starting from the volume data, I still wouldn't suggest -volume-parcel-resampling. Instead, just use the subject's subcortical label volume when making the initial flipped or not flipped cifti files, and use -cifti-resample to get them into a shared grayordinate space, same as I suggested.
Finally, as for edge effects of parcel-constrained smoothing: yes, I expect they are noticeable in our 2mm fwhm data, and a smaller amount of extra smoothing won't make them vanish. Tim On Fri, Sep 1, 2017 at 3:04 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Mike was talking about the effect of using some within parcel smoothing > and some between parcel smoothing so I suggested he make the data from > scratch if he wants to do all between parcel smoothing. I think they > should just smooth within parcels and only add the needed smoothing to get > things up to 3mm FWHM. > > Matt. > > From: Timothy Coalson <tsc...@mst.edu> > Date: Friday, September 1, 2017 at 3:02 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: "Harms, Michael" <mha...@wustl.edu>, Daria Jensen < > dariajen...@gmail.com>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org>, Miriam Klein-Flugge < > mklein0...@googlemail.com> > > Subject: Re: [HCP-Users] clustering of subcortical structures - flipping > and smoothing > > Using that transform that flips X around the origin should put left on > right and right on left, yes. Note, however, that the left and right > parcel ROIs are not the same, so you will have to figure out how to handle > the mismatched edges. > > I would not suggest -volume-parcel-resampling. If you want it back in > cifti in the same subcortical ROIs, the ideal way would be to also create > an X flipped subcortical volume file, then swap left and right labels in it > (probably by -volume-label-export-table, edit to exchange LEFT and RIGHT, > then -volume-label-import), then use -cifti-create-dense-* to make a > flipped cifti, then finally use -cifti-resample to deal with the > nonoverlapping ROI edges by resampling it back to the opposite side > original subcortical ROIs. You could swap the left and right surface data > during this process also. > > The -volume-parcel-smoothing command should not have an "across parcels" > option, that would be what "-volume-smoothing" is for. This option exists > in cifti commands because cifti already contains the parcel ROIs, and we > decided the default would be to treat them separately. > > Tim > > > On Fri, Sep 1, 2017 at 2:11 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > >> I guess I don’t know why one would want to smooth across the known >> boundaries, but the option is available in wb_command -cifti-smoothing. >> One could instead redo the volume mapping to CIFTI with wb_command >> -volume-parcel-resampling using a very small number for the kernel, and >> then apply the chosen wb_command -cifti-smoothing afterwards. There is a >> wb_command -volume-parcel-smoothing that does not have the across parcel >> option, though that would probably be trivial to add. >> >> Matt. >> >> From: "Harms, Michael" <mha...@wustl.edu> >> Date: Friday, September 1, 2017 at 1:56 PM >> To: Matt Glasser <glass...@wustl.edu>, Daria Jensen < >> dariajen...@gmail.com>, "hcp-users@humanconnectome.org" < >> hcp-users@humanconnectome.org> >> >> Cc: Miriam Klein-Flugge <mklein0...@googlemail.com> >> Subject: Re: [HCP-Users] clustering of subcortical structures - flipping >> and smoothing >> >> >> >> @Matt: The minimally preprocessed subcortical data in the CIFTI was >> smoothed with a 2 mm FWHM “parcel-constrained” kernel, right? (i.e, the >> smoothing does not cross boundaries of subcortical structures). In that >> case, if they were to then further smooth the subcortical data, but smooth >> across subcortical boundaries (as they proposed), wouldn’t that potentially >> lead to some odd effects at the boundaries? [I don’t know if you caught >> that part of their proposal…] >> >> >> >> 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 >> <(314)%20747-6173> >> >> St. Louis, MO 63110 Email: >> mha...@wustl.edu >> >> >> >> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of "Glasser, >> Matthew" <glass...@wustl.edu> >> *Date: *Friday, September 1, 2017 at 1:50 PM >> *To: *Daria Jensen <dariajen...@gmail.com>, " >> hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> *Cc: *Miriam Klein-Flugge <mklein0...@googlemail.com> >> *Subject: *Re: [HCP-Users] clustering of subcortical structures - >> flipping and smoothing >> >> >> >> 1. That command for the surface is not quite what you are looking for. >> For the surface, the left and right hemisphere vertices are already in >> register (meaning that vertices with the same number will be in the >> anatomically corresponding location). You would need to translate between >> the CIFTI indices and the GIFTI surface indices to take advantage of that >> however. The easiest way to do this would be to use wb_command >> -cifti-separate and the you can do operations on the resulting GIFTI files. >> >> >> 2. I think if you fed wb_command -volume-resample (on the NIFTI files >> that result from wb_command -cifti-separate) a matrix with the form: >> >> >> >> -1 0 0 0 >> >> 0 1 0 0 >> >> 0 0 1 0 >> >> 0 0 0 1 >> >> >> >> This might accomplish the left right flip in the volume, however Tim >> should confirm if he agrees. >> >> >> >> Matt. >> >> >> >> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Daria >> Jensen <dariajen...@gmail.com> >> *Date: *Friday, September 1, 2017 at 11:47 AM >> *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> *Cc: *Miriam Klein-Flugge <mklein0...@googlemail.com> >> *Subject: *[HCP-Users] clustering of subcortical structures - flipping >> and smoothing >> >> >> >> >> >> Dear HCP list, >> >> >> >> We’re interested in clustering of subcortical structures in the HCP >> resting-state fMRI data and have two questions regarding the pre-processing: >> >> >> >> 1. We’re looking for a way to flip the data of the two hemispheres, >> including subcortical structures, It seems that an option exist to do his >> for the surface (-surface-flip-lr). Which procedure would you recommend >> for flipping the hemispheres of the whole brain, including the volume data? >> >> >> >> 2. Moreover, we’re thinking of applying wb_command -cifti-smoothing to >> the individual dtseries files with a fwhm of 3mm for subcortical structures >> to make the clustering more robust. Our approach would be to smooth across >> subcortical boundaries. What would be your advice? Has anyone got advice >> with regards to the kernel size? And finally, why do we need to indicate a >> left and right surface file in the command? How are these files used the >> smoothing process (and do they have to correspond to the surface from each >> individual)? >> >> >> >> >> >> Thank's a lot! >> >> >> >> Daria Jensen >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> 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
