There isn't really a quick solution, as you need to basically find/replace the values in the file of the duplicate label names with the main values. I'm not sure how this file was generated, so I can't say what procedure was used, but I suppose you could give -cifti-dilate a try and see if you like the result (fair warning: it will bleed into the medial wall).
Tim On Fri, Aug 5, 2016 at 3:27 AM, Salim Arslan <[email protected]> wrote: > Dear Tim, > > Thanks for the follow-up. Could you suggest a quick solution for this that > can do the work until the release of the fixed data file? I am not much > familiar with most of the wb_command,- as you can see in my original post, > I am more of a Matlab person- so perhaps, if you could give me a hint about > how to change those label files, I would really appreciate. A command that > can be used for filling the holes in the 4th map in order to regenerate the > 3rd map would also help. > > Best regards, > Salim > > > ------------------------------ > *From:* Timothy Coalson <[email protected]> > *To:* Salim Arslan <[email protected]> > *Cc:* "[email protected]" <[email protected]> > *Sent:* Friday, August 5, 2016 12:46 AM > *Subject:* Re: [HCP-Users] Extracting Power parcellations from > RSN-networks.32k_fs_LR > > 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 <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 > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > > > > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
