NITRC BioImage Suite Forum: open-discussion

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.

Using BioImagingConnectivity Viewer on fNIRS data

Xenophon Papademetris — Wed, 17 Aug 2022 18:00:41 GMT

You will need some kind of image with the 108 sensors labeled in MNI space as numbers 1 to 108. It does not need to be perfect as all we need this is draw the lines to roughly the correct places (and to sort the regions in some sane order.)

Using BioImaging Connectivity Viewer on fNIRS data

Isabel Nichoson — Wed, 17 Aug 2022 17:58:16 GMT

I'm interested in using BioImaging Connectivity Viewer on whole-head fNIRS data. Obviously since we are working with only 108 channels means that we would have difficulty reverse engineering our data into the 268 parcellations as we lack sufficient resolution. Does anyone know how should best go about creating a new parcellation image? I have a probe file already created. I am just unfamiliar with how to turn that into a functional atlas. Thank you!