Displaying pconn.nii with wb_view

[Yen-Wen Chen]

Hello HCP experts, 

I have some naive questions about displaying images in wb_view.

I generate two .pconn.nii files from a group of 57 subjects from HCP-Aging (for pilot purpose) following steps below, 

   1. demean the individual resting runs 

   2. merge the demeaned dtseries across 4 runs and all 57 subjects (-cifti-merge)

   3. using -cifti-parcellate with (1) Glasser cortical atlas ("RelatedValidation210*CorticalAreas*.32k_fs_LR.dlabel.nii") and with (2) Glasser cortical combining freesurfer subcortical ("RelatedValidation210*CorticalAreas*with_Atlas_ROIs2.32k_fs_LR.dlabel.nii")

   1.4. calculating correlation using -cifti-correlation and generate two .pconn.nii 

I want to display both .pconn.nii using wb_view to obtain the result correlation brain images and matrices. I would like it looks like the Figure 18 from workbench tutorial.

When I open the one with cortical-only pconn (360 x 360), the wb_view only displays "Chart" tab (without "Surface" or "Volume"...).

When I open the one with cortical and subcortical pconn (379 x 379), the wb_view only display a "Volume" and a "Chart" tab. But the "Volume" tab only display the 1st row (in Overlay ToolBox showing "Row: 1" in "Map" column). 

I am wondering if I did something wrong that the wb_view was not able to display correctly? 

Any information and suggestion will be helpful. Thank you.

Best, 
Samantha

[Coalson, Timothy Scott (S&T-Student)]

You need to also open the appropriate surface files (.surf.gii), which contain the surface coordinates, in order to display surface data.  Inflated or very inflated surfaces are generally the most useful for display.

Tim

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From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Sent: Thursday, November 11, 2021 1:51 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Displaying pconn.nii with wb_view

 

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[Yen-Wen Chen]

Hello Tim, 

Thank you for the prompt response. 

One follow-up question, would it be a good idea to use the mesh atlas from the pipeline, such as colin.cerebral.L/R.flat.32k_fa_LR.surf.gii? (for resting functional data) Or would you kindly recommend the surface template that is appropriate to display group data? 

Many thanks, 

Sam. 

[Elam, Jennifer]

Hi Sam,

You could just use the group average Q1-Q6 surface included in the WB Tutorial you've been working with.

Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org

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From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Sent: Thursday, November 11, 2021 3:51 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: tsc...@mst.edu <tsc...@mst.edu>
Subject: Re: [hcp-users] Displaying pconn.nii with wb_view

 

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[Yen-Wen Chen]

Hello Jenn, 

Thank you for the quick response and suggestion. It works well!

Best, 

Sam. 

[Yen-Wen Chen]

Hello, I have a naive question about the color bar of the .pconn.nii. 

Like previously stated, I used the Galsser cortical and Freesurfer subcortical atlas ("Q1-Q6_RelatedValidation210*CorticalAreas*with_Atlas_ROIs2.32k_fs_LR.dlabel.nii") to create the .pconn file (with -cifti-correlation) and then display on wb_view. 

Are the values from -cifti-correlation Pearson correlation r?

The color bar range displayed on wb_view is from -0.478 - 0.478. Does this range make sense? I thought the maximum r value would 1, which would be the correlation with it's own parcel? 

Any information would be very helpful. Thank you.

Best, 
Sam. 

[Glasser, Matt]

Perhaps that is 2 to 98% and you need to change the scaling.

 

Matt.

 

From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Tuesday, November 16, 2021 at 1:02 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Yen-Wen Chen <yen-we...@stonybrook.edu>, "Elam, Jennifer" <el...@wustl.edu>, Timothy Coalson <tsc...@mst.edu>
Subject: Re: [hcp-users] Displaying pconn.nii with wb_view

 

 

Hello, I have a naive question about the color bar of the .pconn.nii. 

 

Like previously stated, I used the Glasser cortical and Freesurfer subcortical atlas ("Q1-Q6_RelatedValidation210*CorticalAreas*with_Atlas_ROIs2.32k_fs_LR.dlabel.nii") to create the .pconn file (with -cifti-correlation) and then display on wb_view. 

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/268a6afa-e4c8-45a6-b942-f2b12f7b8633n%40humanconnectome.org.

[Yen-Wen Chen]

Hi Matt, 

Thank you for your prompt response. That is exactly what it is! 

I did not realize the color bar uses "Abs Pct" (absolute percentage?) and the range is 2 - 98. When I change it to "Full" (does this mean the original value form the .pconn file?), I got -0.345 - 1.

Thank you so much!

Best, 
Sam.  

[Coalson, Timothy Scott (S&T-Student)]

You can also set it to manual to get exactly the range you want.  In general, wb_view doesn't know how you generated a file, and can't "expect" a particular range, it can only look at the data values and, by default, make a guess as to how to give them good contrast.  You can, however, use wb_command -cifti-palette to store palette settings in the file so wb_view will use that instead of the default.

Tim

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From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Sent: Tuesday, November 16, 2021 1:25 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: glas...@wustl.edu <glas...@wustl.edu>; Yen-Wen Chen <yen-we...@stonybrook.edu>

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/961c4081-b487-448b-8312-3482e56b7cbbn%40humanconnectome.org.

[Yen-Wen Chen]

Hi Tim, 

Sorry for the late response. Thank you for your suggestion. 

Can you elaborate this a bit more? Sorry, I am not familiar with how this function would be implemented.

(1) Do I use the .pconn.nii as <cifti-input>? 

(2) <mode> argument: are those options (MODE_AUTO_SCALE, MODE_USER_SCALE, etc.) the same as the options in wb_view "Palette" in Overlay and Map setting (Full, Abs Pct, etc.)? 

Thank you so much.

Best, 

Sam. 

[Coalson, Timothy Scott (S&T-Student)]

Yes, all of those settings are things from the palette settings window in wb_view.  If you save a file in wb_view after changing the palette settings, they will be stored in that file and used next time you open it.  wb_command -cifti-palette is just a way to do that in a script (that is, without loading it into wb_view first).  For instance:

wb_command -cifti-palette <your pconn> MODE_USER_SCALE <your pconn> -neg-user 0 -1 -pos-user 0 1

Tim

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From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Sent: Friday, November 19, 2021 11:54 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Coalson, Timothy Scott (S&T-Student) <tsc...@mst.edu>; Yen-Wen Chen <yen-we...@stonybrook.edu>

[Yen-Wen Chen]

Hi Tim, 

Thank you so much for the clarification! 

Best, 
Sam.