Merge branch 'dev' of github.com:freesurfer/freesurfer into dev

Author: Douglas Greve

freeview/DialogPreferences.cpp

@@ -82,7 +82,7 @@ DialogPreferences::DialogPreferences(QWidget *parent) :
 
 #ifdef Q_OS_MAC
   ui->groupBoxMac->setEnabled(true);
-  ui->groupBoxMac->show();
+  ui->groupBoxMac->hide();
 //  connect(ui->checkBoxMacUnified, SIGNAL(toggled(bool)), mainwnd, SLOT(SetUnifiedTitleAndToolBar(bool)));
   connect(ui->checkBoxCommandKey, SIGNAL(toggled(bool)), mainwnd, SLOT(SetUseCommandControl(bool)));
 #else

freeview/Interactor.cpp

@@ -25,7 +25,7 @@
 #include <QDebug>
 
 #ifdef Q_OS_MAC
-Qt::KeyboardModifier Interactor::CONTROL_MODIFIER = Qt::MetaModifier;
+Qt::KeyboardModifier Interactor::CONTROL_MODIFIER = Qt::ControlModifier;
 Qt::Key Interactor::CONTROL_KEY = Qt::Key_Meta;
 #else
 Qt::KeyboardModifier Interactor::CONTROL_MODIFIER = Qt::ControlModifier;
@@ -53,7 +53,7 @@ void Interactor::SetAction( int nAction )
 void Interactor::SetUseCommandControl(bool b)
 {
 #ifdef Q_OS_MAC
-  if (b)
+  if (true)
   {
     CONTROL_MODIFIER = Qt::ControlModifier;
     CONTROL_KEY = Qt::Key_Control;

mri_synthseg/mri_synthseg

@@ -43,6 +43,7 @@ def main():
     parser.add_argument("--parc", action="store_true", help="(optional) Whether to perform cortex parcellation.")
     parser.add_argument("--robust", action="store_true", help="(optional) Whether to use robust predictions (slower).")
     parser.add_argument("--fast", action="store_true", help="(optional) Bypass some processing for faster prediction.")
+    parser.add_argument("--ct", action="store_true", help="(optional) Clip CT scans in Hounsfield scale to [0, 80]")
     parser.add_argument("--vol", help="(optional) Output CSV file with volumes for all structures and subjects.")
     parser.add_argument("--qc", help="(optional) Output CSV file with qc scores for all subjects.")
     parser.add_argument("--post", help="(optional) Posteriors output(s). Must be a folder if --i designates a folder.")
@@ -144,6 +145,7 @@ def main():
         names_qc=names_qc_labels,
         cropping=args.crop,
         topology_classes=topology_classes,
+        ct=args.ct,
     )
 
 
@@ -174,7 +176,8 @@ def predict(path_images,
             labels_qc,
             names_qc,
             cropping,
-            topology_classes):
+            topology_classes,
+            ct):
     '''
     Prediction pipeline.
     '''
@@ -258,6 +261,7 @@ def predict(path_images,
 
             # preprocessing
             image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i],
+                                                                         ct=ct,
                                                                          crop=cropping,
                                                                          min_pad=min_pad,
                                                                          path_resample=path_resampled[i])
@@ -491,7 +495,7 @@ def prepare_output_files(path_images, out_seg, out_posteriors, out_resampled, ou
            out_qc, unique_qc_file
 
 
-def preprocess(path_image, n_levels=5, crop=None, min_pad=None, path_resample=None):
+def preprocess(path_image, ct, n_levels=5, crop=None, min_pad=None, path_resample=None):
 
     # read image and corresponding info
     im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True)
@@ -526,6 +530,8 @@ def preprocess(path_image, n_levels=5, crop=None, min_pad=None, path_resample=No
         crop_idx = None
 
     # normalise image
+    if ct:
+        im = np.clip(im, 0, 80)
     im = rescale_volume(im, new_min=0, new_max=1, min_percentile=0.5, max_percentile=99.5)
 
     # pad image

mris_convert/mris_convert.cpp

@@ -43,6 +43,8 @@
 
 #include "compilerdefs.h"
 
+#include "MRISurfOverlay.h"
+
 #define __COMBINESURFS_TAKE_INFILE2 0
 
 //------------------------------------------------------------------------
@@ -488,26 +490,9 @@ main(int argc, char *argv[])
 
 static void __convertOverlayFile(MRIS *mris, const char *fcurv, char *out_fname)
 {
-  if (MRISreadCurvatureFile(mris, fcurv) != NO_ERROR)
-  {
-    printf("ERROR reading curvature file %s\n", fcurv);
-    exit(1);
-  }
-
-  int type = MRISfileNameType(out_fname) ;
-  if (type == MRIS_ASCII_FILE)
-  {
-    mrisWriteAsciiCurvatureFile(mris, out_fname);
-    //writeAsciiCurvFile(mris, out_fname) ;
-  }
-  else if (type == MRIS_GIFTI_FILE)
-  {
-    MRISwriteGIFTI(mris, NIFTI_INTENT_SHAPE, out_fname, fcurv);
-  }
-  else
-  {
-    MRISwriteCurvature(mris, out_fname) ;
-  }
+  MRISurfOverlay *fsOverlay = new MRISurfOverlay();
+  fsOverlay->read(fcurv, TRUE, mris);
+  fsOverlay->write(out_fname, mris);
 }
 
 

utils/mrisurf_io.cpp

@@ -5062,10 +5062,18 @@ int MRISreadCurvatureFile(MRI_SURFACE *mris, const char *sname)
     frame = MRISgetReadFrame();
 
     // ??? why read the volume twice ???
-    TempMRI = MRIreadHeader(fname, mritype);
+    //TempMRI = MRIreadHeader(fname, mritype);
+    //if (TempMRI == NULL) {
+    //  return (ERROR_BADFILE);
+    //}
+
+    // MRI_CURV_FILE will be read in as MRI - MRISreadCurvAsMRI();
+    // MRI_MGH_FILE - mghRead()
+    TempMRI = MRIread(fname);
     if (TempMRI == NULL) {
       return (ERROR_BADFILE);
     }
+
     if (TempMRI->nframes <= frame) {
       printf("ERROR: attempted to read frame %d from %s\n", frame, fname);
       printf("  but this file only has %d frames.\n", TempMRI->nframes);
@@ -5076,14 +5084,8 @@ int MRISreadCurvatureFile(MRI_SURFACE *mris, const char *sname)
       printf("ERROR: number of vertices in %s does not match surface (%d,%d)\n", sname, nv, mris->nvertices);
       return (1);
     }
-    MRIfree(&TempMRI);
+    //MRIfree(&TempMRI);
 
-    // MRI_CURV_FILE will be read in as MRI - MRISreadCurvAsMRI();
-    // MRI_MGH_FILE - mghRead()
-    TempMRI = MRIread(fname);
-    if (TempMRI == NULL) {
-      return (ERROR_BADFILE);
-    }
     vno = 0;
     curvmin = 10000.0f;
     curvmax = -10000.0f; /* for compiler warnings */