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.
> dtseries.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
>>>
>>>
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>>
>>
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