I am feeling confused. If "brainordinate" is what is shown in the information box when you click on a vertex, then mine does match the 96484 grayordinates. I also have "brainordinates" on the medial wall (e.g., VERTEX CortexRight 433 is on the medial wall). Let me know if I should look elsewhere for the brainordinates.
Thanks, Cherry On Sun, Mar 22, 2015 at 5:24 PM, Glasser, Matthew <[email protected]> wrote: > I’m pretty sure that wb_view indices match ciftiopen if you use > “Identify Brainordinate.” As I said, the medial wall is not defined in any > of the dense timeseries files you might wish to use in your analysis (even > if it was, the data inside it wouldn’t be valid as it wouldn’t be cerebral > cortex). Let me know if you don’t follow the instructions below for > converting your dlabel files into 91282 grayordinates space. > > Peace, > > Matt. > > From: Yizhou Ma <[email protected]> > Date: Sunday, March 22, 2015 at 5:19 PM > To: Matt Glasser <[email protected]>, "[email protected]" > <[email protected]> > > Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read > > 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. 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