NITRC BioImage Suite Forum: open-discussion

RE: Usingconnectome-based predictive modeling to predict individual behavior frombrain connectivity

Xenophon Papademetris — Fri, 03 Jan 2025 15:39:20 GMT

(From Dr. Xilin Shen.)

The "predict_behavior" is a function that takes the matrices and behavioral scores as inputs and outputs the performance r value of the cross validation.

An example of "prediction_behavior" function and the associated Matlab script can be found in this new update
https://www.nitrc.org/frs/download.php/17884/ConnectomeCodeShen_OHBM.zip

RE: Using connectome-based predictive modeling to predict individual behavior from brain connectivity

irislr — Wed, 25 Dec 2024 11:53:07 GMT

Originally posted by chirokoff:
<blockquote>[i]Originally posted by Yingxue Gao:[/i][quote]Hi, I was trying to run the "permutation_test_example.m" scripts, but I was not able to find the "predict_behavior" function. Dose anybody know? Thank you, Yingxue[/quote] [color=#000000]Hi,[/color] [color=#000000]I have the same problem. Did you find the solution ?[/color] [color=#000000]Thank you,[/color] [color=#000000]Valentine [/color]</blockquote>
Hi, I'm having the same issue. Based on the Shen et al. 2017 paper it seems this function is never actually provided in the example scripts. I believe 'predict_behavior' is meant to return the correlation coefficient between the predicted and true behavioral measures; is there a specific way this should be implemented, or does any correlation work?

How to calculate intrinsic connectivity distributionï¼ˆICDï¼‰

Xenophon Papademetris — Tue, 02 Apr 2024 14:31:02 GMT

We have not ported this over to the web version. The download server for the old version crashed but if you email me directly (Xenophon dot Papademetris at yale dot edu) and mention what OS you need this for, I can send you a download link.

How to calculate intrinsic connectivity distribution（ICD）

Yong Han — Tue, 02 Apr 2024 7:55:01 GMT

Dear everyone:

I’ve found many papers on calculating the intrinsic connectivity distribution mentioning the use of the BioImage Suite. However, it seems that this feature is no longer available in the latest web version, and the older versions are nowhere to be found.

Could anyone please advise on a solution?

Thank you very much!

BioimageSuite visualization with a new parcellation image

Liana Okudzhava — Sat, 18 Mar 2023 17:09:42 GMT

Dear Experts,

I'm using connectome-based predictive modeling to investigate structural connectivity using diffusion imaging.
When visualizing the output in Bioimage Suite, there is an option to load my own parcellation image, which should be a NIFTI file in the MNI space. However, when I try to load my parcellation, I get the following error:
(Bad image loaded parcels_wholebrain_mni.nii.gz dim=168,258,211,1,1, sp=0.85,0.75,0.75,1,1 orient=RAS type=float. Must beundefined).
Do you have any idea why this could be the case, and what I could potentially do to fix it?
As an alternative to a parcellation image, the manual says I could also upload MNI coordinates as a txt file, but this option is not available at all in the menu.
Attached is the parcellation file just in case.

I appreciate your feedback and thank you in advance.

Best regards,
Liana Okudzhava

How to getten-Networks labels of Shen atlas?

Xenophon Papademetris — Fri, 14 Oct 2022 20:08:01 GMT

Sorry for the delay. Here is the label description spreadsheet https://www.dropbox.com/s/e5bqmiy41z4xd5y/Shen268_10network.xlsx?dl=0

How to get ten-Networks labels of Shen atlas?

yihe weng — Tue, 04 Oct 2022 15:39:02 GMT

Hi,

Is there any label information of ten networks for Shen 268 atlas? Becasue there are 10 networks, including Medial Frontal (MF), Frontoparietal (FPN), Default Mode (DMN), Motor (MOT), Visual I (Vis I), Visual II Network (Vis II), Visual Association (VAs), Salience (SAL), Subcortical (SC), and Cerebellar (CBL) in the head map plotting in the Connviewer, and also can be found in Greene et al.(2018).

However, the network label of Shen atlas online just has 8 networks. Does anyone know how to get the network label for 10 networks?

Thank you very much!

Best wishes,
Yihe

RE: SOS filepositive

Xenophon Papademetris — Mon, 12 Sep 2022 15:11:49 GMT

Could you send me the file directly (xenophon dot papademetris at yale dot edu)

RE: SOS file positive

hildaura — Sun, 11 Sep 2022 14:39:35 GMT

[i]Originally posted by Hildaura Zulantay:[/i][quote]Hello:

Greetings to all.

A question:

Can somebody help me?

The positive file reads the first row and 303 columns. Sure, I need to be the 268x268 reading of data entered.

Thanks.

Hildaura

PS: File attached.[/quote]

SOS file positive

hildaura — Sun, 11 Sep 2022 14:37:33 GMT

Hello:

Greetings to all.

A question:

Can somebody help me?

The positive file reads the first row and 303 columns. Sure, I need to be the 268x268 reading of data entered.

Thanks.

Hildaura

PS: File attached.