Merge pull request #66 from Deep-MI/dev

Update for compatibility with Numpy 2.

README.md

@@ -190,9 +190,7 @@ A list of changes is available [here](CHANGES.md).
 This repository contains multiple branches, reflecting the ongoing
 development of the toolbox. The two primary branches are the main branch
 (`stable`) and the development branch (`dev`). New features will first be added
-to the development branch, and eventually be merged with the main branch. You
-are currently on the main branch. To go to the development branch, select it
-from the drop-down menu on the top left, or [click here](https://github.com/Deep-MI/fsqc/tree/dev).
+to the development branch, and eventually be merged with the main branch. 
 
 ### Roadmap
 

VERSION

@@ -1 +1 @@
-2.1.0
+2.1.1

fsqc/createSurfacePlots.py

@@ -93,7 +93,7 @@ def createSurfacePlots(SUBJECT, SUBJECTS_DIR, SURFACES_OUTDIR, VIEWS, FASTSURFER
     # check if annotation has labels that are not included in the colortable
     if any(annotL[0] == -1):
         # prepend colortable and update indices
-        ctabL = np.concatenate((np.mat([127, 127, 127]), annotL[1][:, 0:3]), axis=0)
+        ctabL = np.concatenate((np.asmatrix([127, 127, 127]), annotL[1][:, 0:3]), axis=0)
         indsL = annotL[0] + 1
     else:
         ctabL = annotL[1][:, 0:3]
@@ -104,7 +104,7 @@ def createSurfacePlots(SUBJECT, SUBJECTS_DIR, SURFACES_OUTDIR, VIEWS, FASTSURFER
     # check if annotation has labels that are not included in the colortable
     if any(annotR[0] == -1):
         # prepend colortable and update indices
-        ctabR = np.concatenate((np.mat([127, 127, 127]), annotR[1][:, 0:3]), axis=0)
+        ctabR = np.concatenate((np.asmatrix([127, 127, 127]), annotR[1][:, 0:3]), axis=0)
         indsR = annotR[0] + 1
     else:
         ctabR = annotR[1][:, 0:3]