Yes it does seem the first of four columns has 8 distinct numbers. As a side note, is there any released HCP resting state data on a 164k mesh or are they all 32k mesh?
Thank you, David Hartman On Mon, Jul 17, 2017 at 6:19 PM, Timothy Coalson <tsc...@mst.edu> wrote: > You can get a text file containing the label names and keys for a map by > using -cifti-label-export-table. It appears that this will have extraneous > labels in it due to how the file was generated, but you can ignore the key > values that aren't used. > > If you count the number of unique values in one column of the cifti file > you opened, you will probably get the number you are expecting. It is > simply that the values are not 1-7, but an arbitrary set of integers. > > The -cifti-parcellate command will automatically use the first map in the > label file to compute within-label averages for its labels. It is probably > not what you want to use to simply examine the label map. I'm not sure why > it ended up with 8 rather than 7 parcels, though. As a side effect, you > could use "wb_command -cifti-parcel-mapping-to-label" to generate a label > file that should be much less cluttered, but we may have better advice on > this soon... > > Tim > > > On Mon, Jul 17, 2017 at 4:51 PM, David Hartman <dhartman1...@gmail.com> > wrote: > >> Since calling in MATLAB: “ciftiopen('RSN-networks.32k_fs_LR.dlabel.nii', >> 'workbench\bin_windows64\wb_command.exe')” gives me a matrix with 4 >> columns whose range is beyond the 17 or 7 corresponding to their functional >> grouping, I have resorted to using wb-command hoping to get right >> labelling. >> >> >> >> *Question:* Which wb-command should I use to read the labels and see for >> the 32k mesh which networks the nodes belong to (ie. 1 to 7)? >> >> >> >> I tried using wb_command -cifti-parcellate rfMRI_REST1_LR_Atlas_MSMAll.dt >> series.nii RSN-networks.32k_fs_LR.dlabel.nii COLUMN out.ptseries.nii, >> but out.ptseries.nii returns a matrix 8×1200. But I am hoping for >> something 32k×1 for the correct labelling, where each row is a number >> between 1 and 7 or 17 corresponding to the group the node belongs to. >> >> >> >> >> >> Hope it is not too confusing. >> >> >> >> Thank you, >> >> David Hartman >> >> On Mon, Jul 17, 2017 at 3:09 PM, Harms, Michael <mha...@wustl.edu> wrote: >> >>> >>> Hi, >>> There are actually 4 different maps in that file. If you load it into >>> Workbench, the name associated with each map tells you what each map is. >>> >>> 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 David >>> Hartman <dhartman1...@gmail.com> >>> Date: Monday, July 17, 2017 at 12:21 PM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: Re: [HCP-Users] mapping HCP data into 7 functional networks >>> (using Thomas Yeo parcellation) >>> >>> Hi, >>> >>> >>> >>> *Background:* >>> >>> Regarding the labels file, “RSN-networks.32k_fs_LR.dlabel.nii” which I >>> thought should contain the 7 and 17 network parcellation, this file has a >>> matrix of size 64984×4. What do the numbers in the 4 columns represent (ie. >>> 1st column has a max of 44 and 4th column a max of 26). I was expecting >>> a single column that took values from 1 to 17 or 1 to 7 mapping each vertex >>> to its grouping in the functional networks. >>> >>> >>> >>> >>> >>> *Question:* >>> >>> How should I understand these 4 columns and their connection to >>> functional network parcellation? >>> >>> >>> >>> Thank you, >>> >>> David Hartman >>> >>> On Fri, Jul 14, 2017 at 2:27 PM, David Hartman <dhartman1...@gmail.com> >>> wrote: >>> >>>> Hi, >>>> >>>> >>>> >>>> *Background:* >>>> >>>> Regarding the parcellation of the cortex into functional networks (“The >>>> organization of the human cerebral cortex estimated by intrinsic functional >>>> connectivity,” Yeo et al.) Yeo breaks up the cortex into 7 networks. >>>> However, his cortical data has 163842 vertices, while the HCP data only has >>>> 59412 vertices. >>>> >>>> >>>> >>>> *Question:* >>>> >>>> I am looking to map the HCP data into these 7 networks, but I don’t see >>>> a way to get the data into the same format as Yeo’s data (ie. 163842 >>>> vertices) to use his mapping. >>>> >>>> 1. Does anyone know of a way to convert HCP data into the same format >>>> as Yeo’s data to use his mapping or a direct way to map the HCP data to 7 >>>> networks? >>>> >>>> >>>> >>>> Any help would be much appreciated. >>>> >>>> >>>> >>>> Thank you, >>>> >>>> David Hartman >>>> >>>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> 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. 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