NITRC BioImage Suite Forum: help

RE: Importing Shen 268 parcellation atlas into CONN

yao ge — Fri, 28 Jun 2024 1:02:24 GMT

<p><em>Originally posted by kjacobs:</em></p>
<blockquote>Hi All, I'm attempting to upload the Shen 268 parcellation atlas into CONN and experiencing some issues with the ROI labels. After checking formatting and consistent file names between the .nii and .csv files, did anyone do anything further? I'm I missing a step? Thank you in advance, Katie Jacobs</blockquote>
<p>Hi Katie,</p>
<p>I've came across the same problem. Have you figured out how to solve it? Thanks a lot!</p>

RE: BioimageSuite visualization with a new parcellation image

Marie Santillo — Fri, 12 Jan 2024 9:59:03 GMT

<p>I am also having the same problem. Was anyone able to find a solution for this?</p>

BioImage Suite Electrode Editor: Dimensions limit

zoel — Sat, 05 Aug 2023 19:38:10 GMT

<p>Hello all,</p>
<p>   I am trying to label a depth electrode (intracranial electrode localization) with 18 contacts in the Electrode Editor. I have been able to do this successfully up to 16 electrodes. However, at 18 electrodes, it will cap me at 16 and only allow me to label the last 16 electrodes (3-18). As you can see in the image attached, I put 1x18 as the dimensions for the electrode. But only 16 electrodes appear in the Electrode Arrangement Box to assign coordinates to electrodes in the CT image. </p>
<p>Anyone know a way around this issue?</p>
<p>Thanks,<br>Zoe</p>

BioImage Suite - import parcellation image into Connviewer

Mathilde Argote — Tue, 11 Jul 2023 13:57:10 GMT

<p>Dear experts, </p>
<p>I am trying to import a parcellation image (.nii) into the connectivity visualization tool. I clicked the button "Advance" > "Import parcellation image" and chose the atlas that I used for my analyses (atlas.nii). This atlas is the one used by default by the CONN toolbox for resting-state fMRI. </p>
<p>The visualization tool does not recognize the image. Indeed, when I select this atlas to import, nothing happens.</p>
<p>Could you please explain what could be wrong with this file? I have uploaded it along with this post. </p>
<p>Thank you very much,</p>
<p>Mathilde</p>

Matrix Ordering and FDR Test Verification

Francisco Diego Rabelo da Ponte — Mon, 10 Jul 2023 13:32:49 GMT

<div class="elementToProof">I have a couple of questions regarding the Bio Suite Website that I would like to kindly ask you. I searched on the website and it wasn't clear to me. </div>
<div class="elementToProof">
<ol data-editing-info="{"orderedStyleType":6,"unorderedStyleType":1}" data-listchain="__List_Chain_41">
<li>Firstly, when uploading positive and negative matrices to the website, should I order the matrices in ascending order, starting from node 1 and ending at node 268? </li>
<li>Secondly, I would like to know how I can verify the values of the False Discovery Rate (FDR) test on the website. Could you please provide guidance on accessing this information? </li>
</ol>
<div>Thank you for your assistance. I look forward to hearing from you. </div>
<div>Best regards,</div>
</div>
<div class="elementToProof"> </div>

BioimageSuite visualization with a new parcellation image

Liana Okudzhava — Sat, 18 Mar 2023 17:08:32 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

Importing Shen 268 parcellation atlas into CONN

kjacobs — Sat, 08 Dec 2018 1:55:16 GMT

Hi All,

I'm attempting to upload the Shen 268 parcellation atlas into CONN and experiencing some issues with the ROI labels. After checking formatting and consistent file names between the .nii and .csv files, did anyone do anything further? I'm I missing a step?

Thank you in advance,

Katie Jacobs

can't load my gradient directions in bioImage suite

Fan Jiachen — Mon, 26 Nov 2018 15:01:30 GMT

Dear friends ,I found it difficult to specify gradient directions by creating my own set .I have created a text file using my text editor and input my directions(32) accroding to the format mentioned by BioImage Suite manual.However ,after laoded in the gradients pane ,the new set of diretions doesn't appear in the list and nothing in the preview window.I hope for your reply .thanks!
I have saved this text file with a .dat extension,but it doesn't work.I need your help!Thank you again.

RE: Installation Problem

Max Nentwich — Thu, 14 Sep 2017 16:14:06 GMT

Hi,

I have got a similar error:

vtk: error while loading shared libraries: libhistory.so.5: cannot open shared object file: Error 40

I tried the suggested solution, but that did not help.

Does anyone have an idea on how to solve this?

Thanks,
Max Nentwich

RE: another installation problem

nilew — Fri, 14 Apr 2017 18:21:05 GMT

Just ran into this issue, and accidentally solved it while fixing another issue! I also am running Windows 7.

[b]Background[/b]
I used to only have one major user account on this desktop, but I had to create a second one recently. BioImage Suite still opens just fine in the old account, but I would run into the error you have with the new account. I tried uninstalling and reinstalling from the new account, but that did not fix things. I also tried giving all possible permissions to my account and making sure I had administrative access etc.

[b]Solution[/b]
When trying to fix a completely separate issue for Git, I went to the Windows Start Menu, typed in "Environment Variables" and clicked on "Edit environment variables for your account". In "User variables for [username]", I added a new variable called "HOME" with the value "C:\Users\[you_username_here]". This seemed to magically fix things for me.