cifti-gradient for creating effect size borders

[Joseph Orr]

I was hoping to get some clarity on the process of creating borders of effect size gradients following a previous post.

I first created a gradient file of my group-level cohen map:

wb_command -cifti-gradient results_cohen.dscalar.nii COLUMN results_cohen_gradient.dscalar.nii -left-surface S1200.L.midthickness_MSMAll.32k_fs_LR.surf.gii -left-corrected-areas L_area.func.gii -right-surface S1200.R.midthickness_MSMAll.32k_fs_LR.surf.gii -right-corrected-areas R_area.func.gii

Here is an image of my effect size map with the gradient map overload on top. I thresholded the map till I saw something that looked sensible.

I proceeded to draw borders following the gradients:

I saved the borders as a new file, and then proceeded to try to optimize the borders following Matt's suggestion in the post I linked to above. However, I'm not sure if I am doing this correctly. I drew another border around the existing borders - you can see the red new border on top of the saved borders in pink. I'll make sure I get a cleaner border when I proceed. When I try to finish and optimize this border I see an error that I don't follow.

I'd appreciate any clarification on the border optimization procedure. I didn't see anything in the previous HCP Course materials.

Thanks,

Joe

--

Joseph M. Orr, Ph.D.

Assistant Professor

Department of Psychological and Brain Sciences

Texas A&M Institute for Neuroscience

Texas A&M University

College Station, TX

he/him/his
https://tamu.zoom.us/my/josephorr

[Harwell, John]

Hi Joe,

 

This is a bit of a guess from looking at the source code.  The algorithm may expect to find two borders in the ROI but it is only finding one border named “GradientBorders”.  In addition, there should be borders with the same name(s) in the Border Pair file.  If you don’t have two borders in the ROI, you might try unchecking the “Border Pair File” checkbox and see if that helps.

 

Further down in the dialog under “Save Results”, the “path” is empty.  Use the Browse button on the right to set the path for the output file.  This should fix the part of the error message beginning with “Save Results…”.

 

John Harwell

 

 

From: 'Joseph Orr' via HCP-Users <hcp-...@humanconnectome.org>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, May 18, 2022 at 11:33 AM
To: HCP Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] cifti-gradient for creating effect size borders

 

* External Email - Caution *

I was hoping to get some clarity on the process of creating borders of effect size gradients following a previous post.

 

I first created a gradient file of my group-level cohen map:

wb_command -cifti-gradient results_cohen.dscalar.nii COLUMN results_cohen_gradient.dscalar.nii -left-surface S1200.L.midthickness_MSMAll.32k_fs_LR.surf.gii -left-corrected-areas L_area.func.gii -right-surface S1200.R.midthickness_MSMAll.32k_fs_LR.surf.gii -right-corrected-areas R_area.func.gii

 

Here is an image of my effect size map with the gradient map overload on top. I thresholded the map till I saw something that looked sensible.

I proceeded to draw borders following the gradients:

 

I saved the borders as a new file, and then proceeded to try to optimize the borders following Matt's suggestion in the post I linked to above. However, I'm not sure if I am doing this correctly. I drew another border around the existing borders - you can see the red new border on top of the saved borders in pink. I'll make sure I get a cleaner border when I proceed. When I try to finish and optimize this border I see an error that I don't follow.

 

I'd appreciate any clarification on the border optimization procedure. I didn't see anything in the previous HCP Course materials.

 

Thanks,

Joe

 

--

Joseph M. Orr, Ph.D.

Assistant Professor

Department of Psychological and Brain Sciences

Texas A&M Institute for Neuroscience

Texas A&M University

College Station, TX

he/him/his
https://tamu.zoom.us/my/josephorr

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

The border you draw for the optimization process should contain large parts of the two areas that are on either side of the border being optimized.  It is not a guess at the new border location.  Basically, you should "circle" a relatively straight piece of border, and it will optimize the part within the "circle".

I think the border pair is only for doing statistics.  I would not expect them to be in a separate input file, though - maybe it was a hack to go back and do statistics without redoing the optimization.

Tim

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From: Harwell, John <jhar...@wustl.edu>
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Subject: Re: [hcp-users] cifti-gradient for creating effect size borders

 

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[Joseph Orr]

I see, thanks for the clarification. I'll give that a try.

On Wed, May 18, 2022, 4:36 PM Coalson, Timothy Scott (S&T-Student) <tsc...@mst.edu> wrote:

The border you draw for the optimization process should contain large parts of the two areas that are on either side of the border being optimized. It is not a guess at the new border location. Basically, you should "circle" a relatively

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