On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> Thank you,
>
>
> How can I turn the ROIs into a label file?
>
You can use -cifti-find-clusters if you just want spatial contiguity to
define where ROIs should be considered separate, then use
-cifti-label-import to make them into a dlabel file.

> Also, how can I simply get a list of the ROIs with some information like
> cluster extent and peak voxel to be able to identify what part(s) of the
> brain each ROI is covering?
>
A single coordinate isn't a faithful representation of the cluster.  You
can make a figure showing the clusters displayed on the brain (for
instance, choose two of: beta maps, significance outlines, area outlines),
and hopefully also provide the unthresholded beta and z maps for others to
use.

You can get cluster extent info with -cifti-weighted-stats.

If the question you want to ask is "which areas are involved", you could do
a parcellated analysis instead of a cluster analysis.

> Thank you,
>
> Michael
> ------------------------------
> *From:* Timothy Coalson <tsc...@mst.edu>
> *Sent:* Monday, September 19, 2016 4:48:28 PM
> *To:* Michael F.W. Dreyfuss
> *Cc:* hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] ROIs and Betas from Cifti Data
>
> The wb_command -cifti-weighted-stats command with -mean is probably what
> you want (outputs a number to the command line), though you'll need to have
> each ROI as a separate file and run it separately for each of them.
> Alternatively, if you turned the ROIs into a label file, you could get
> -cifti-parcellate to make a file where each parcel contains the answer for
> an ROI.
>
> Tim
>
>
> On Mon, Sep 19, 2016 at 3:26 PM, Michael F.W. Dreyfuss <
> mid2...@med.cornell.edu> wrote:
>
>> Hello, I have run palm with TFCE on my group level data successfully for
>> a task based fMRI study (yay!), and I would like to be able to identify
>> ROIs from my cifti data (both surface and volume). I then want to
>> extract subject level beta weights for a given condition from those ROIs to
>> relate those betas to behavior (offline). Are there simple ways to: 1)
>> identify regions implicated on the group level and 2) extract subject-level
>> beta weights from them, such as with wb_command?
>>
>>
>> Thank you,
>>
>> Michael
>>
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>
>

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