Error in running toolbox

[strokeresearch]

Hi

I'm new to stroke lesion segmentation. I've installed SynthStrokeSPM in the latest version of MATLAB as per the guidance here. I'm encountering an error (as detailed below). I'd be grateful for any advice.

19-Dec-2024 15:01:33 - Running 'SynthStroke'
Warning: Name is nonexistent or not a directory: /Users/caitlin/Downloads/spm12/toolbox/SynthStrokeSPM

In path (line 109)
In addpath>doPathAddition (line 126)
In addpath (line 90)
In spm_SynthStroke (line 8)
In spm_cfg_SynthStroke>spm_run_synthstroke (line 79)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53) 


19-Dec-2024 15:01:33 - Failed 'SynthStroke'
Error using spm_SynthStroke (line 18)
Model file not found: /Users/caitlin/Downloads/spm12/toolbox/SynthStrokeSPM/data/unet.mat
In file "/Users/caitlin/Downloads/spm12/toolbox/SynthStrokeSPM-main/private/spm_SynthStroke.m" (???), function "spm_SynthStroke" at line 18.
In file "/Users/caitlin/Downloads/spm12/toolbox/SynthStrokeSPM-main/private/spm_cfg_SynthStroke.m" (???), function "spm_run_synthstroke" at line 79.

The following modules did not run:
Failed: SynthStroke

[liamchalcroft]

Hi, many thanks for your interest in the tool!

The line here:

Warning: Name is nonexistent or not a directory: /Users/caitlin/Downloads/spm12/toolbox/SynthStrokeSPM

suggests that the tool is not in the correct location. Can you confirm that you have SPM12 already installed in this mentioned path, and have added the downloaded folder to the specified 'toolbox' subfolder?

[strokeresearch]

Thanks, Liam.

I can confirm that SPM12 is installed in this path and the toolbox is added to the subfolder.

I followed the instructions as below and the error happens when I run the batch.

Open SPM12
Navigate to "Batch" → "SPM" → "Tools" → "SynthStroke"
In the batch editor:
Select your input image(s)
Choose your desired options
Set the output directory (optional)
Run the batch

[liamchalcroft]

Does running the line ls /Users/caitlin/Downloads/spm12/toolbox/SynthStrokeSPM within MATLAB show you the expected folder contents for this tool?

• If it does, then the error you have received should not occur and it is worth checking that SPM12 / the toolbox folder have been added to your MATLAB path.
• If it doesn't, then the toolbox has not been placed in the correct location, or perhaps there are multiple SPM installs on your computer and the tool is in a different spm12/toolbox/ to that of the current running SPM.

[strokeresearch]

Thanks. The SynthStrokeSPM folder I downloaded was saved as 'SynthStrokeSPM-main'. When I changed the folder name there was some progress but still encountered an error further along.

---

20-Dec-2024 21:38:38 - Running job #1

20-Dec-2024 21:38:38 - Running 'SynthStroke'
Warning: Variable 'net' originally saved as a dlnetwork cannot be instantiated as an object and will be read in as a uint32.

In spm_SynthStroke (line 16)
In spm_cfg_SynthStroke>spm_run_synthstroke (line 79)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
Rescaling image to [0, 1]...
Elapsed time is 0.022082 seconds.
Image rescaling completed.
Performing histogram normalization...
Elapsed time is 0.269721 seconds.
Histogram normalization completed.
Z-scoring histogram normalized image...
Elapsed time is 0.017378 seconds.
Histogram normalized image z-scored.
Preparing input volume for prediction...
Elapsed time is 0.070185 seconds.
Input volume prepared.
20-Dec-2024 21:38:40 - Failed 'SynthStroke'
Undefined function 'dlarray' for input arguments of type 'string'.
In file "/Users/caitlin/spm12/toolbox/SynthStrokeSPM/private/stroke_segmentation.m" (???), function "stroke_segmentation" at line 71.
In file "/Users/caitlin/spm12/toolbox/SynthStrokeSPM/private/spm_SynthStroke.m" (???), function "spm_SynthStroke" at line 38.
In file "/Users/caitlin/spm12/toolbox/SynthStrokeSPM/private/spm_cfg_SynthStroke.m" (???), function "spm_run_synthstroke" at line 79.

The following modules did not run:
Failed: SynthStroke