Another thing is that when I look at a grayordinate in wb_view, it gives the index of that grayordinate and its statistics. I can use the index number to find the corresponding grayordinate easily if I am using 96484 grayordiantes from ft_read_cifti, but not as easy if I am using ciftiopen.
On Sun, Mar 22, 2015 at 5:05 PM, Glasser, Matthew <[email protected]> wrote: > Yes, ciftiopen gives the correct number of grayordinates. If you need > to correct your dlabel files, you can use wb_command -cifti-separate to get > out the GIFTI label files and then use wb_command -cifti-create-label with > the correct medial wall ROIs—any subject’s > ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii > will do. If you also want to put zeros in the subcortical structures, you > can additionally use as the parcel-volume any subject’s > ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz and as the > label volume the same volume where you’ve set all voxels to zero. > > Peace, > > Matt. > > From: Yizhou Ma <[email protected]> > Date: Sunday, March 22, 2015 at 4:56 PM > To: Matt Glasser <[email protected]> > Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read > > Hi Matthew, > > I am trying to calculate the correspondence between the HCP ICA > parcellations with other parcellations (e.g. Yeo 2011, Power 2011). > > It is ciftiopen that is giving me 91282 grayordinates. > > Best, > Cherry > > On Sun, Mar 22, 2015 at 4:52 PM, Glasser, Matthew <[email protected] > > wrote: > >> For ft_read_cifti, that sounds like a bug, as there are only a total of >> 91282 grayordinates at 2mm spacing (the medial wall is not defined in the >> CIFTI standard grayordinates space). As far as matching the dlabel files >> with the rest of the CIFTI files, it is true that you need to remove the >> medial wall (and they don’t include any subcortical structures either). >> What is it that you are trying to do with the dlabel files? >> >> Peace, >> >> Matt. >> >> From: Yizhou Ma <[email protected]> >> Date: Sunday, March 22, 2015 at 4:44 PM >> To: "[email protected]" <[email protected]> >> Subject: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read >> >> Dear HCP experts, >> >> I'd like to report what seems to me a problem with ciftiopen. When I >> opened a .dscalar.nii file with ft_read_cifti, I got 96854 grayordinates. >> Yet when I used ciftiopen, I got 91282 grayordiantes. It seems to me that >> ciftiopen automatically left out where there is a "NaN" in the .dscalar >> file. This has been a problem for me since I've been trying to use some of >> the .dlabel files offered by HCP, which come with 64984 surface >> grayordinates when opened with ciftiopen, medial wall included. It took me >> a while to realize that my results are not matching up because the >> discorrespondence in indices. >> >> Given that ciftiopen does not read the labelnames and label values from >> cifti files, I think it can be confusing when it left out "NaN" values on >> the medial wall when reading .dscalar files. >> >> Best, >> Cherry >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > > ------------------------------ > > 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. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
