RESPAN Windows GUI opens but Run produces no output

[ardennorthchaim]

Hi @lahammond — thanks for making RESPAN public, it’s a really impressive tool. I’m trying to run the Windows GUI (RESPAN_v0_9_99) on Windows 11 with an RTX 3060 (nvidia-smi works, GPU visible), but I’m running into an issue where the GUI opens normally and allows selection of valid data and nnU-Net model directories, yet clicking Run produces no output: no GPU activity, no logs, no output folders, and no visible error. I’ve tried running from Command Prompt (not Anaconda), moving RESPAN to C:, removing read-only attributes, taking ownership and granting full permissions, running as administrator, disabling Defender temporarily, and testing with a minimal local dataset, but the behavior is unchanged. Is this a known Windows/permissions issue, or is there a recommended way to surface backend startup errors or logs for the packaged GUI? Happy to provide more details if helpful — thanks again for sharing the tool.

[lahammond]

Hi @ardennorthchaim,

Thanks for reaching out. Could you confirm whether you’re running the latest GUI release (v1.0.00)? A few similar reports have turned out to be caused by older builds. The newest version is linked in the repo README: https://github.com/lahammond/RESPAN

On Windows (10 and 11), RESPAN shouldn’t require any special permissions. One thing to note is that the first run after downloading the app or after moving it to a new folder can produce extra initialization messages. After that, you should see the GPU details in the log and a successful initialization message on subsequent runs.

Also, please double-check the dataset structure. RESPAN expects datasets to be organized into subfolders, each containing an analysis_settings file (from the provided template). However, if there are issues related to how the files are organized, the log will still show an error indicating the issue.

Let me know how you go with the newer release.
Luke

[HerediJudit]

Hi @lahammond ,

I am really interested in your analyzer tool as well. It seems really cool.

I had the same problem as @ardennorthchaim. I am using the latest version available here, on Windows 10 Pro x64, with an NVIDIA GeForce GTX 1650 (4 GB) graphics card (I know it is not the recommended one, but the GUI opens normally for me, too).
First, I tried to test the software using your example spinning disk confocal dataset, but clicking on Run resulted in nothing. No logging, no error message. I followed your video guide.

Have you managed to identify what might be causing the problem in the case of @ardennorthchaim?
Thanks in advance for your help,

Judit

[lergov]

Hello,

I am also having the same issue. I am using latest release on Windows 11 with an 19-14900K and RTX 4090. Has anyone found a solution?

UPDATE:
I just installed the previous release and the program ran as expected.

[HerediJudit]

The problem has been resolved for me as well. The organization of the image files to be analyzed was incorrect. Even if you only have one test group, the images must be placed in a subfolder (even if it's just a single image). With this adjustment, the latest version runs for me.

However, regarding the models, Model1A is currently not working and throws errors. On the other hand, it runs perfectly with Model1B.

[lahammond]

Hi all,

Thanks for reaching out and for your interest in RESPAN.

In most cases, RESPAN will run without issue. However, when problems like these arise, we've found it is usually the result of one of a small number of easily addressable setup issues rather than a GPU or permissions problem.

The most common issues we observe:

1. Input data not organized into subfolders within the input directory
RESPAN expects the input directory to contain subfolders, even when processing a single image or test group, because the software is designed for batch processing. This may not be intuitive unless following the guide or the note below the folder input field in the GUI. If image files are placed directly in the input directory, RESPAN will run but will not process them. In the current release, this may appear as though nothing is happening because the progress bar updates, but a log file is not generated. We have improved logging for this in an upcoming update.

2. Dataset directories need to contain an Analysis_Settings file
Due to the batch processing design and support for multiple experiments in one run. Each folder needs to contain one of these files. We handle this elegantly in the upcoming update, so that if this file is missing, it will automatically generate in the folder based on the settings provided in the GUI.

3. Spaces in the file path
If there is a space anywhere in the path to RESPAN, the dataset, or the model directory, this can cause startup failures. For example, paths under user accounts such as C:\Users\A Name... may trigger this issue. This is addressed in an upcoming release.

4. Using OneDrive or other cloud-synced/shared Windows folders
On some Windows 11 systems, files are saved by default in OneDrive-synced locations. We have seen cases where running RESPAN from cloud or shared folder causes problems with reading/writing files. We recommend using a local folder for RESPAN installation on the machine instead (e.g. Program Files)

5. Model folder selected incorrectly or downloaded incompletely
A few issues have been caused by incomplete model downloads or by selecting the wrong folder in RESPAN after extracting the model files. To avoid this issue, please ensure you are selecting the model folder that begins with Dataset..., not the parent folder that contains it. If the model is downloaded in multiple ZIP files, they need to be fully extracted into a single directory.

We also recommend using RESPAN v1.0, rather than older releases. Regarding Models, Model1B generally works best for most applications. We have an improved version of this model that we will upload later today.

I hope this is helpful. Thanks, everyone, for sharing this feedback, and thanks to Judi for helping resolve these issues, too.

Best,
Luke