-cifti-cross-correlation is for when you want to correlate between two
different files. If you want roi-to-roi correlations, it is not the best
way to get them.
The easy way to get roi-to-roi correlations is to use -cifti-parcellate and
then -cifti-correlation. However, you first need to convert your ROIs into
a cifti dlabel file. To do that, first use
-cifti-create-dense-from-template to convert your ROI files to cifti
dscalar, using some standard 91282 grayordinate file as the template, then
concatenate them. You then need to use -cifti-reduce, computing both the
INDEXMAX and the MAX reductions, and then use -cifti-math to multiply the
INDEXMAX file by whether the MAX file is nonzero at that location
(something like 'index * (max > 0)'). The point of this is to make a
single map where each ROI has a different nonzero integer value, and where
there is no ROI, it is zero. This file can then be used in
-cifti-label-import to make the dlabel file.
Tim
On Fri, Sep 21, 2018 at 7:22 AM, Xinyang Liu <xinyang_ie...@163.com> wrote:
> Dear Matt,
>
> Thank you very much for your prompt reply.
>
> I will have a try according to your suggestions.
>
> Best regards,
> Xinyang
>
>
> At 2018-09-21 19:37:13, "Glasser, Matthew" <glass...@wustl.edu> wrote:
>
> 1. ${StudyFolder}/${Subject}/MNINonLinear/Results/${
> fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii
> 2.1 wb_command -cifti-parcellate after wb_command -metric-merge wb_command
> -metric-label-import and wb_command -cifti-create-dense-label
> 2.2 See above
> 2.3 wb_command -cifti-correlation on the individual subject dense
> timeseries above (ideally after demeaning, potentially variance
> normalizing, and concatenating across the runs in each subject—see
> wb_shortcuts).
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu <
> xinyang_ie...@163.com>
> Date: Friday, September 21, 2018 at 4:00 AM
> To: HCP 讨论组 <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] rfMRI connecitivity
>
> Dear HCP experts,
>
> Hi. We are trying to compute resting state fMRI connectivity between
> several ROIs for single individuals. The surface ROIs (.func.gii) were
> acquired from task fMRI data. The plan is to compute the averaged rfMRI
> timeseries within each ROI, and then compute their correlations.
>
> We have several questions to ask:
>
> 1. The HCP user manual suggests to use dtseries.nii data in the FIX
> folder. However, there are two rfMRI dtseries.nii files there, one with
> MSMALL, and one without it. Which one is more recommended to use?
>
> 2. We are quite lost in using the wb_commands. By checking previous
> emails, it seems that we could use "-cifti-parcellate" to compute the
> ROI-wise averaged time series. But before that, it seems that we also need
> to create some .dlabel files. So,
>
> (1) which command should we use to extract dtseries covered by those
> .func.gii ROIs?
>
> (2) To compute the averaged time series, should we merge all ROIs
> together in one cortical surface or compute one by one? Because the
> .func.gii surface ROIs are saved as separate files.
>
> (3) We would like to compute rfMRI connectivity for single
> individuals, not group average. Is -cifti-cross-correlation the correct
> choice?
>
> Look forward to your kind guidance. Thank you very much.
>
> Best regards,
> Xinyang
>
>
>
>
>
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