Extracting average time course using Glasser atlas

129 views
Skip to first unread message

Daniel Panitz

unread,
Dec 2, 2021, 7:15:35 AM12/2/21
to HCP-Users
Dear experts,
I have the anatomical and functional (at rest) images of a set of subjects that were scanned several years ago, and I want to extract an average time course for each region according to the Glasser atlas, in order to produce a region x time matrix for each subject.
Since this data is in legacy format (i.e., only T1w images), I used fmriprep and ciftify to convert them into cifti format.
My question is this: how do I extract average time courses according to the Glasser atlas? Is it achieved by using wb_command -cifti-parcellate?
Does it need the Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii file?
Also, should it be by row or by column? I did not understand that about the cifti format -could you explain it to me, or direct me to a good explanation?
Thank you very much.
Best regards,
Daniel.

Glasser, Matt

unread,
Dec 2, 2021, 8:12:08 AM12/2/21
to hcp-...@humanconnectome.org

Yes.

We usually recommend this file: https://balsa.wustl.edu/file/3VLx 

COLUMN, https://www.nitrc.org/projects/cifti/

 

Matt.

--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/bf5e55a6-ec1d-4688-b072-361e4ee8c835n%40humanconnectome.org.

 

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. If you have received this email in error, please immediately notify the sender via telephone or return mail.

Coalson, Timothy Scott (S&T-Student)

unread,
Dec 2, 2021, 11:49:57 AM12/2/21
to hcp-...@humanconnectome.org
wb_command -cifti-help has a brief explanation of the cifti format:


Tim

From: Glasser, Matt <glas...@wustl.edu>
Sent: Thursday, December 2, 2021 7:12 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] Extracting average time course using Glasser atlas
 
WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.

Daniel Panitz

unread,
Dec 4, 2021, 9:02:09 AM12/4/21
to HCP-Users, tsc...@mst.edu
Dear experts,
Thank you very much for your answers.
However,  it seems I understand even less than I originally thought, as I find many different .dscalar.nii files (such as SUBJECT.sulc.32k_fs_LR.dscalar.nii,  SUBJECT  .thickness.32k_fs_LR.dscalar.nii,  SUBJECT.EdgeDistortion_MSMSulc.32k_fs_LR.dscalar.nii), and I am not sure which one fits my needs.
I am sorry to bother you with basic questions, but could you please tell me which file to use, or direct me to an explanation regarding the uses of each of these files?
Best regards,
Daniel. 

Glasser, Matt

unread,
Dec 4, 2021, 9:12:40 AM12/4/21
to hcp-...@humanconnectome.org, tsc...@mst.edu

What is it that you are trying to do?

Matt.

Daniel Panitz

unread,
Dec 4, 2021, 9:45:00 AM12/4/21
to HCP-Users, glas...@wustl.edu, tsc...@mst.edu
I am trying to extract an average BOLD signal for each region in the atlas, and set that up as a region x time matrix.
Daniel,

Glasser, Matt

unread,
Dec 4, 2021, 10:25:47 AM12/4/21
to hcp-...@humanconnectome.org, tsc...@mst.edu

In what data, HCP data?

Matt.

Daniel Panitz

unread,
Dec 4, 2021, 11:44:12 AM12/4/21
to HCP-Users, glas...@wustl.edu, tsc...@mst.edu
No, these are subjects that were scanned several years ago as part of a different study.
Daniel.

Glasser, Matt

unread,
Dec 4, 2021, 11:50:27 AM12/4/21
to Daniel Panitz, HCP-Users, tsc...@mst.edu

Did you process with the HCP Pipelines?

Matt.

James Thompson

unread,
Dec 4, 2021, 12:05:39 PM12/4/21
to hcp-...@humanconnectome.org
Hi Daniel,
You might find the Cole-Anticevic tools helpful:  https://github.com/ColeLab/ColeAnticevicNetPartition

There is Matlab and python code that should do what you want.

Jim

--

Daniel Panitz

unread,
Dec 4, 2021, 12:07:31 PM12/4/21
to HCP-Users, glas...@wustl.edu, tsc...@mst.edu, Daniel Panitz
This dataset only contains T1w and resting-state scans, so I was under the impression that it will not fit the HCP Pipelines.
I used fmriprep (https://fmriprep.org/en/stable/) to preprocess the data, and ciftify (https://github.com/edickie/ciftify) to convert it from nifti format to HCP compatible cifti format (using ciftify_recon_all for the anatomical data and ciftify_subject_fmri for the functional data).
Now that I look at the ciftify website (https://edickie.github.io/ciftify/#/), I see a function that might suit my needs, ciftify_meants, which I missed previously.
Daniel.

Glasser, Matt

unread,
Dec 4, 2021, 12:09:31 PM12/4/21
to Daniel Panitz, HCP-Users, tsc...@mst.edu

Sounds good though it is worth noting that the HCP Pipelines now have a legacy mode for if you do not have a T2w scan.  Lacking a field map is a more severe issue that no tool is able to handle well, regardless of the claims out there.

Reply all
Reply to author
Forward
0 new messages