eebrown / lst Goto Github PK

It has been working well without an issue.
Recently, I encountered the following error:

Error using fprintf
Invalid file identifier. Use fopen to generate a valid file identifier.
In file "/home/xubuntu/spm12/toolbox/LST/ps_LST_lpa.m" (???), function "ps_LST_lpa" at line 117.

The following modules did not run:
Failed: LST: Lesion segmentation (LPA)

However, the files do not have any issues. They are nii files, not compressed.
I tried to process other sets of files that had previously been processed successfully with LST. However, I encountered the same error. I am confused.

Could you explain what might be the issue?

Sincerely,
-SC

I've run LPA supplying both a T1-w and FLAIR image for WMH segmentation on an AD dataset. I see NaNs appearing in several voxels after inspecting outputs and am confused by what they mean. From the code, it looks like NaNs aren't necessarily "0" voxels, but they also aren't necessarily WMHs either (especially since some of the NaNs I inspect in FSLEyes capture some large WMHs). I am wondering if there is an approach that might appropriately deal with NaNs - set them to 0 in cases where it's unlikely to be a WMH, but give them a non-zero value in cases where it's more likely to be a WMH?

Any assistance would be greatly appreciated!

Hi Eric,
I am trying to understand how I can run this matlab script (ps_LST_LPA) without specifying the T1 images as reference, running MATLAB via the linux command line. Here is the code for one subject:

time /data/SOFTWARE/MATLAB/R2015b/bin/matlab -debug -nosplash -nodesktop -r "try ps_LST_lpa('sub01-FLAIR.nii', '');catch e;display(e.message);end;quit"

Where '' is where Vref would go, but because I don't want the T1 to be included, I left this blank. The command-line output I received was:

This is LST www.statistical-modeling.de/lst.html
Algorithm: Lesion prediction algorithm (LPA)
If anything goes wrong: LST_log_20230316_125624.txt
Number of jobs to process: 1
Coregister to reference images: no
Cannot CD to (Name is nonexistent or not a directory).

real 0m11.239s
user 0m9.801s
sys 0m0.888s

I also tried setting Vref as a variable to 0, but still wasn't able to get this to work!

Do you have any suggestions?

Regards :)