I see. In my WB 1.0 the information window offers "Select Brainordinates"
function. Yet I can only select the surface vertices there.
On Sun, Mar 22, 2015 at 5:40 PM, Glasser, Matthew <glass...@wusm.wustl.edu>
wrote:
> Those are vertex IDs that don’t match grayordinate Ids (even in your
> space they won’t match for the right hemisphere). There should be a select
> brainordinate option somewhere in that window that you can use to get a
> specific brainordinate. The whole information window needs a bit of a
> rewrite though and the development version of wb_view I have in front of me
> has already had some of the changes made to it so I cannot tell you exactly
> where to look.
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma <maxxx...@umn.edu>
> Date: Sunday, March 22, 2015 at 5:33 PM
> To: Matt Glasser <glass...@wusm.wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
>
> 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 <glass...@wusm.wustl.edu
> > 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 <maxxx...@umn.edu>
>> Date: Sunday, March 22, 2015 at 5:19 PM
>> To: Matt Glasser <glass...@wusm.wustl.edu>, "
>> hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>
>> 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 <
>> glass...@wusm.wustl.edu> 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 <maxxx...@umn.edu>
>>> Date: Sunday, March 22, 2015 at 4:56 PM
>>> To: Matt Glasser <glass...@wusm.wustl.edu>
>>> 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 <
>>> glass...@wusm.wustl.edu> 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 <maxxx...@umn.edu>
>>>> Date: Sunday, March 22, 2015 at 4:44 PM
>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>> 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
>>>>
>>>> _______________________________________________
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>>>>
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>>>
>>>
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