gcc 8.4 updates (freesurfer#843)

ayendiki · Feb 5, 2021 · 07a667a · 07a667a
1 parent 290fa49
commit 07a667a
Show file tree

Hide file tree

Showing 40 changed files with 580 additions and 153 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,7 @@ CTestTestfile.cmake
 Makefile
 *.[oa]
 ld_map.txt
+install_manifest.txt
 
 # generated help files
 *.help.xml.h
@@ -49,6 +50,8 @@ anatomicuts/AnatomiCuts.bin
 anatomicuts/AnatomiCuts_correspondences.bin
 anatomicuts/streamlineFilter.bin
 anatomicuts/trk_tools.bin
+AntsDenoiseImageFs/AntsDenoiseImageFs
+AntsN4BiasFieldCorrectionFs/AntsN4BiasFieldCorrectionFs
 check_siemens_dir/check_siemens_dir
 connectgraph/connectgraph
 diffusion_tool/diffusion_tool
@@ -82,6 +85,7 @@ mri_and/mri_or
 mri_annotation2label/mri_annotation2label
 mri_aparc2aseg/mri_aparc2aseg
 mri_aparc2wmseg/mri_aparc2wmseg
+mri_aparc2aseg/mri_surf2volseg
 mri_apply_inu_correction/mri_apply_inu_correction
 mri_aseg_edit_reclassify/mri_aseg_edit_reclassify
 mri_aseg_edit_train/mri_aseg_edit_train
@@ -91,6 +95,7 @@ mri_bc_sc_bias_correct/mri_bc_sc_bias_correct
 mri_bias/mri_apply_bias
 mri_bias/mri_compute_bias
 mri_binarize/mri_binarize
+mri_brainvol_stats/mri_brainvol_stats
 mri_build_priors/mri_build_priors
 mri_ca_label/mri_ca_label
 mri_ca_normalize/mri_ca_normalize
@@ -217,6 +222,7 @@ mri_polv/mri_polv
 mri_probe_ima/mri_probe_ima
 mri_probedicom/mri_probedicom
 mri_reduce/mri_reduce
+mri_refine_seg/mri_refine_seg
 mri_register/mri_register
 mri_relabel_hypointensities/mri_relabel_hypointensities
 mri_relabel_nonwm_hypos/mri_relabel_nonwm_hypos
@@ -234,6 +240,7 @@ mri_robust_register/mri_robust_register
 mri_robust_register/mri_robust_template
 mri_sbbr/mri_sbbr
 mri_seg_diff/mri_seg_diff
+mri_seg_overlap/mri_seg_overlap
 mri_segcentroids/mri_segcentroids
 mri_seghead/mri_seghead
 mri_segment/mri_segment
@@ -270,6 +277,7 @@ mri_volsynth/mri_volsynth
 mri_warp_concat/mri_warp_concat
 mri_warp_convert/mri_warp_convert
 mri_watershed/brain_volume/mri_brain_volume
+mri_watershed/brain_volume/mri_brain_volume_test
 mri_watershed/mri_validate_skull_stripped
 mri_watershed/mri_watershed
 mri_wbc/mri_wbc
@@ -281,6 +289,7 @@ mris2rgb/mris2rgb
 mris_BA_segment/mris_BA_segment
 mris_add_template/mris_add_template
 mris_anatomical_stats/mris_anatomical_stats
+mris_annot_diff/mris_annot_diff
 mris_annot_to_segmentation/mris_annot_to_segmentation
 mris_apply_reg/mris_apply_reg
 mris_aseg_distance/mris_aseg_distance
@@ -340,9 +349,11 @@ mris_longitudinal_surfaces/mris_longitudinal_surfaces
 mris_make_average_surface/mris_make_average_surface
 mris_make_face_parcellation/mris_make_face_parcellation
 mris_make_map_surfaces/mris_make_map_surfaces
+mris_make_surfaces/mris_autodet_gwstats
 mris_make_surfaces/mris_exvivo_surfaces
 mris_make_surfaces/mris_make_surfaces
 mris_make_surfaces/mris_mef_surfaces
+mris_make_surfaces/mris_place_surface
 mris_make_surfaces/mris_refine_surfaces
 mris_make_template/mris_make_template
 mris_map_cuts/mris_map_cuts
@@ -452,3 +463,7 @@ utils/fsPrintHelp
 utils/gifti_test
 utils/gifti_tool
 utils/xmlToHtml
+
+# testdata
+*/testdata
+Testing
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -129,6 +129,9 @@ if(NOT APPLE)
     NAMES libgfortran.a gfortran)
   find_library(BLAS_LIBRARIES NAMES libopenblas.a libblas.a)
   find_library(LAPACK_LIBRARIES NAMES liblapack.a)
+  find_library(QUADMATH_LIBRARIES
+    HINTS /usr/lib64 /usr/lib /usr/lib/gcc/*/*/
+    NAMES libquadmath.a)
 endif()
 
 # -------- armadillo --------

diff --git a/attic/mri_cal_normalize/CMakeLists.txt b/attic/mri_cal_normalize/CMakeLists.txt
@@ -0,0 +1,7 @@
+project(mri_cal_normalize)
+
+include_directories(${FS_INCLUDE_DIRS})
+
+add_executable(mri_cal_normalize mri_cal_normalize.cpp)
+target_link_libraries(mri_cal_normalize utils)
+install(TARGETS mri_cal_normalize DESTINATION bin)
diff --git a/mri_ca_normalize/mri_cal_normalize.cpp → ...c/mri_cal_normalize/mri_cal_normalize.cpp b/mri_ca_normalize/mri_cal_normalize.cpp → ...c/mri_cal_normalize/mri_cal_normalize.cpp
diff --git a/mri_ca_normalize/CMakeLists.txt b/mri_ca_normalize/CMakeLists.txt
@@ -8,7 +8,3 @@ target_link_libraries(mri_ca_normalize utils)
 install(TARGETS mri_ca_normalize DESTINATION bin)
 
 add_test_script(NAME mri_ca_normalize_test SCRIPT test.sh DEPENDS mri_ca_normalize)
-
-add_executable(mri_cal_normalize mri_cal_normalize.cpp)
-target_link_libraries(mri_cal_normalize utils)
-install(TARGETS mri_cal_normalize DESTINATION bin)
diff --git a/mri_ca_normalize/mri_ca_normalize.cpp b/mri_ca_normalize/mri_ca_normalize.cpp
@@ -1341,10 +1341,16 @@ find_control_points
 
   if (mri_ctrl)
   {
-    sprintf(fname, "%s_init_label%d.labels.mgz", fname_only, label) ;
+    int req = snprintf(fname, STRLEN, "%s_init_label%d.labels.mgz", fname_only, label) ;
+    if (req >= STRLEN) {
+      std::cerr << __FUNCTION__ << ": Truncation on line " << __LINE__ << std::endl;
+    }
     printf("writing initial sample points for %s to %s\n", cma_label_to_name(label), fname); 
     MRIwriteFrame(mri_ctrl, fname, 0) ;
-    sprintf(fname, "%s_init_label%d.priors.mgz", fname_only, label) ;
+    req = snprintf(fname, STRLEN, "%s_init_label%d.priors.mgz", fname_only, label) ;
+    if (req >= STRLEN) {
+      std::cerr << __FUNCTION__ << ": Truncation on line " << __LINE__ << std::endl;
+    }
     printf("writing initial label priors for %s to %s\n", cma_label_to_name(label), fname); 
     MRIwriteFrame(mri_ctrl, fname, 1) ;
     MRIfree(&mri_ctrl) ;

diff --git a/mri_coreg/mri_coreg.cpp b/mri_coreg/mri_coreg.cpp
@@ -1826,7 +1826,10 @@ MRI *MRIconformNoScale(MRI *mri, MRI *mric)
   // Map input to geometry template
   mric = MRIresample(mri, mritmp, SAMPLE_NEAREST);
 
-  sprintf(mric->fname,"%s/Conformed",mri->fname);
+  int req = snprintf(mric->fname,STRLEN,"%s/Conformed",mri->fname);
+  if (req >= STRLEN) {
+    std::cerr << __FUNCTION__ << ": Truncation on line " << __LINE__ << std::endl;
+  }
   MRIfree(&mritmp);
 
   return(mric);

diff --git a/mri_edit_segmentation/mri_edit_segmentation.cpp b/mri_edit_segmentation/mri_edit_segmentation.cpp
@@ -250,6 +250,9 @@ edit_hippocampus(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled) {
           switch (label) {
           case Left_Cerebral_White_Matter:
             left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           case Right_Cerebral_White_Matter:
             dgray = distance_to_label(mri_out_labeled,
                                       left ? Left_Cerebral_Cortex :
@@ -271,8 +274,14 @@ edit_hippocampus(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled) {
                         left ? Left_Cerebral_Cortex : Right_Cerebral_Cortex,
                         left ? Left_Cerebral_White_Matter : Right_Cerebral_White_Matter) ;
             }
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           case Left_Hippocampus:
             left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           case Right_Hippocampus:
             dgray = distance_to_label(mri_out_labeled,
                                       left ? Left_Cerebral_Cortex :
@@ -349,6 +358,9 @@ edit_hippocampus(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled) {
           }
           case Left_Cerebral_Cortex:
             left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           case Right_Cerebral_Cortex:
             dup = distance_to_label(mri_out_labeled,
                                     left ?  Left_Hippocampus :
@@ -604,6 +616,9 @@ edit_amygdala(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled) {
           switch (label) {
           case Left_Cerebral_Cortex:
             left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           case Right_Cerebral_Cortex:
             dup = distance_to_label(mri_out_labeled,
                                     left ?  Left_Amygdala :
@@ -882,6 +897,9 @@ edit_lateral_ventricles(MRI *mri_in_labeled, MRI *mri_T1, MRI *mri_out_labeled)
           switch (label) {
           case Left_Inf_Lat_Vent:
             left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           case Right_Inf_Lat_Vent:
             dwhite = distance_to_label(mri_out_labeled,
                                        left ? Left_Cerebral_White_Matter :

diff --git a/mri_edit_segmentation_with_surfaces/mri_edit_segmentation_with_surfaces.cpp b/mri_edit_segmentation_with_surfaces/mri_edit_segmentation_with_surfaces.cpp
@@ -649,6 +649,9 @@ relabel_hypointensities(MRI *mri, MRI *mri_inputs,
 	    	 */  
 	   break ;
 	}
+#if __GNUC__ >= 8
+        [[gnu::fallthrough]];
+#endif
         case Left_WM_hypointensities:
         case Right_WM_hypointensities: // check to see if it's outside ribbon and change it to gm
           if (gca)  // if we have a gca, check to make sure gm is possible here

diff --git a/mri_edit_wm_with_aseg/mri_edit_wm_with_aseg.cpp b/mri_edit_wm_with_aseg/mri_edit_wm_with_aseg.cpp
@@ -332,6 +332,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
             break ;
           }
 
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           /* !!! no break - erase unknown if it is surrounded by only  unknowns */
 
           /* erase these  labels */
@@ -373,6 +376,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
         case Right_non_WM_hypointensities:
 	  if (fcd)
 	    break ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Left_Lesion:
         case Right_Lesion:
         case WM_hypointensities:
@@ -440,6 +446,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
             MRIvox(mri_filled, x, y, z) = AUTO_FILL ;
             non++ ;
           }
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Left_Inf_Lat_Vent:
         case Right_Inf_Lat_Vent:
           xi = (label ==  Left_Inf_Lat_Vent) ?  mri_wm->xi[x+1] :  mri_wm->xi[x-1] ; // lateral
@@ -588,6 +597,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
           break ;
         case Left_Hippocampus:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Hippocampus:
         {
           int xi ;
@@ -783,6 +795,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
 
         case Left_Lateral_Ventricle:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Lateral_Ventricle:
           olabel = left ? Left_Cerebral_White_Matter : Right_Cerebral_White_Matter ;
           if (neighborLabel(mri_seg, x, y, z, 2, olabel) > 0)
@@ -879,6 +894,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
         {
         case Left_Cerebral_Cortex:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Cerebral_Cortex:
         case Unknown:
           // look for voxels that are lateral to amygdala, and inf to wm. Should be filled
@@ -1025,6 +1043,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
           case Left_Hippocampus:
           case Left_Amygdala:
             left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
           case Right_Inf_Lat_Vent:
           case Right_Hippocampus:
           case Right_Amygdala:
@@ -1230,6 +1251,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
         {
         case Left_Cerebral_Cortex:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Cerebral_Cortex:
           if (MRIvox(mri_wm, x, y, z) >= MIN_WM_VAL)
           {
@@ -1449,6 +1473,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
         {
         case Left_Cerebral_Cortex:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Cerebral_Cortex:
           // make sure we aren't on the medial edge of hippo
 #if 0
@@ -1526,6 +1553,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
         {
         case Left_Cerebral_Cortex:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Cerebral_Cortex:
           // make sure we aren't on the medial edge of hippo
 #if 0
@@ -1815,6 +1845,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
         {
         case Left_Cerebral_White_Matter:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Cerebral_White_Matter:
           hlabel = left ?  Left_Hippocampus : Right_Hippocampus ;
           // if there is any hippo superior to this label, turn it on
@@ -1863,6 +1896,9 @@ edit_segmentation(MRI *mri_wm, MRI *mri_T1, MRI *mri_seg)
         case Left_Hippocampus:
         case Left_Amygdala:
           left = 1 ;
+#if __GNUC__ >= 8
+  [[gnu::fallthrough]];
+#endif
         case Right_Hippocampus:
         case Right_Amygdala:
         case Right_Inf_Lat_Vent:

diff --git a/mri_fill/mri_fill.cpp b/mri_fill/mri_fill.cpp
@@ -3186,8 +3186,10 @@ main(int argc, char *argv[])
        "%s: could not read SUBJECTS_DIR from environment",Progname) ;
     strcpy(subjects_dir, cp) ;
 
-    sprintf(fname, "%s/%s/mri/transforms/%s.m3d", subjects_dir,sname,
-            atlas_name) ;
+    int req = snprintf(fname, STRLEN, "%s/%s/mri/transforms/%s.m3d", subjects_dir,sname, atlas_name);
+    if (req >= STRLEN) {
+      std::cerr << __FUNCTION__ << ": Truncation on line " << __LINE__ << std::endl;
+    }
     m3d = MRI3DreadSmall(fname) ;
     if (!m3d)
       ErrorExit(ERROR_NOFILE,
@@ -3202,7 +3204,10 @@ main(int argc, char *argv[])
       MRIwrite(mri_p_ventricle, "p_left_ventricle.mgz") ;
     }
 
-    sprintf(fname, "%s/%s/mri/T1", subjects_dir,sname) ;
+    req = snprintf(fname, STRLEN, "%s/%s/mri/T1", subjects_dir, sname);
+    if (req >= STRLEN) {
+      std::cerr << __FUNCTION__ << ": Truncation on line " << __LINE__ << std::endl;
+    }
     mri_T1 = MRIread(fname) ;
     if (!mri_T1)
       ErrorExit(ERROR_NOFILE, "%s: could not read T1 volume %s\n",