Using -cifti-separate on the original cifti file and viewing in wb_view looks identical to the original. However, I think I see what is going on, after getting a hint from the way you reset the color scheme - the file has 2 labels named "a3_Default_mode", and similar for other labels, and turning one of them off reveals these holes.
What has happened is that someone has set the names and colors of two label values to be identical (except for a space on the end of one, to slip past the uniqueness tests on the label names), but they are actually different integers in those patches. I don't know how this happened, as map 4 doesn't have this difference in values. We should probably fix this in the data file. Tim On Thu, Aug 4, 2016 at 3:44 AM, Salim Arslan <[email protected]> wrote: > Hi Tim, > > Thanks for your attention. > > After your message, I also thought the problem was about the order of the > hemisphere in the cifti file. However, after running wb_command > -file-information -no-map-info I can confirm that the order is correct. > Here is the output: > > Name: RSN-networks.32k_fs_LR.dlabel.nii > Type: Connectivity - Dense Label > Structure: CortexLeft CortexRight > Data Size: 1.04 Megabytes > Maps to Surface: true > Maps to Volume: false > Maps with LabelTable: true > Maps with Palette: false > Number of Rows: 64984 > Number of Columns: 4 > Volume Dim[0]: 0 > Volume Dim[1]: 0 > Volume Dim[2]: 0 > Palette Type: None > CIFTI Dim[0]: 4 > CIFTI Dim[1]: 64984 > ALONG_ROW map type: LABELS > ALONG_COLUMN map type: BRAIN_MODELS > Has Volume Data: false > CortexLeft: 32492 out of 32492 vertices > CortexRight: 32492 out of 32492 vertices > > > I do not think anotherCii has also nothing to do with this, as it is just > a cii file with the same row dimensionality (64984x1). > > Following the suggestion in your other message, I have extracted the > hemisphere-specific full-surface label files using wb_command > -cifti-separate with the -label repeatable option and saved the output in a > gii file. The result was the same. > > One thing I forgot to mention and might be important is that, among 4 > parcellations stored in RSN-networks.32k_fs_LR.dlbal.nii, only the > holes-filled power labels (3rd column) has this problem. The others are > just fine. This also makes me think that dlabel file, at least partly, was > generated in an unusual way. Perhaps someone involved in the generation of > the tutorial data package or the aforementioned BALSA study can shed light > on this. > > Salim > > > > ------------------------------ > *From:* Timothy Coalson <[email protected]> > *To:* Salim Arslan <[email protected]> > *Cc:* "[email protected]" <[email protected]> > *Sent:* Wednesday, August 3, 2016 9:36 PM > *Subject:* Re: [HCP-Users] Extracting Power parcellations from > RSN-networks.32k_fs_LR > > First, the size of 64984 shows that the cifti file in question did not > have the medial wall masked out internally, which is likely the starting > point for these problems. I don't know how medialMask is defined, but if > it isn't 32492 elements long (in this case), then that will cause another > problem, as the break between left and right data will be in the wrong > place. > > If you really didn't do any steps between defining labelsL and labelsR, > and anotherCii was made as a copy of that same cii variable, then I don't > know how it managed to mess things up, though, unless this cifti file also > managed to have right hemisphere before left hemisphere (the format > supports this, but we have tried to be consistent with the order - the lack > of a medial wall mask indicates this dlabel file was generated in an > unusual way, though). You can use "wb_command -file-information > -no-map-info" to see the order of structures in the cifti file. > > Tim > > > On Wed, Aug 3, 2016 at 11:22 AM, Salim Arslan <[email protected]> > wrote: > > Hello, > > I am trying to get Power parcellations out of > RSN-networks.32k_fs_LR.dlabel.nii, that comes with the "Brain Analysis > Library of Spatial maps and Atlases (BALSA) database study" ( > https://balsa.wustl.edu/study/show/WG33). It is also part of the tutorial > dataset. > > I did what I have been always doing for extracting data from CIFTI files > in Matlab. Using ciftiopen, I obtained the cii object, which in this case, > contains the cdata matrix of size 64984x4. The 3rd column here corresponds > to the holes-filled Power parcellations. To extract those for both > hemispheres, I simply split up the 64984 vector and masked out the medial > wall vertices and then saved the labels back to CIFTI. > > cii = ciftiopen('RSN-networks.32k_fs_LR.dlabel.nii', wb_command); > cdata = cii.cdata; > parcellation = cdata(:,3); > labelsL = cifti(1:length(medialMask)); > labelsR = cifti(length(medialMask)+1:end); > anotherCii.cdata = [labelsL;labelsR]; > ciftisave(anotherCii,'power.dlabel.nii',wb_command) > > However when I visualized the labels on workbench, I noticed some holes > (with random labels) in many parcels. Please see the attached figure for > clarification. > > I assume this is something to do with the medial masking, but cannot > figure out what is wrong. Any help is appreciated. > > Thanks for your attention. > > Best regards, > Salim > > -- > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
