Better error reporting if Xvfb is not installed.

Author: chrisgorgo

examples/smri_cbs_skullstripping.py

@@ -11,17 +11,17 @@
 wf = pe.Workflow("skullstripping")
 
 mask = pe.Node(JistIntensityMp2rageMasking(), name="masking")
-mask.inputs.inSecond = "/scr/adenauer1/7T_TRT/pilot/data/OK2T140312_093516.SEPT/nifti/S4_MP2RAGE_5_3_TR5000_iPAT=2_INV2.nii"
-mask.inputs.inQuantitative = "/scr/adenauer1/7T_TRT/pilot/data/OK2T140312_093516.SEPT/nifti/S7_MP2RAGE_5_3_TR5000_iPAT=2_UNI_Images.nii"
-mask.inputs.inT1weighted = "/scr/adenauer1/7T_TRT/pilot/data/OK2T140312_093516.SEPT/nifti/S6_MP2RAGE_5_3_TR5000_iPAT=2_T1_Images.nii"
+mask.inputs.inSecond = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_INV2.nii.gz"
+mask.inputs.inQuantitative = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_UNI.nii.gz"
+mask.inputs.inT1weighted = "/Users/filo/7t_trt/niftis/sub001/session_1/MP2RAGE_T1.nii.gz"
 mask.inputs.outMasked = True
 mask.inputs.outMasked2 = True
 mask.inputs.outSignal = True
 mask.inputs.outSignal2 = True
 
 skullstrip = pe.Node(MedicAlgorithmSPECTRE2010(), name="skullstrip")
 skullstrip.inputs.outStripped = True
-skullstrip.inputs.maxMemoryUsage = 6000
+skullstrip.inputs.xDefaultMem = 6000
 
 wf.connect(mask, 'outMasked', skullstrip, 'inInput')
 wf.run()

nipype/interfaces/base.py

@@ -978,16 +978,22 @@ def run(self, **inputs):
                         version=self.version)
         try:
             if self._redirect_x:
-                vdisplay_num = _search_for_free_display()
-                xvfb_cmd = ['Xvfb', ':%d' % vdisplay_num]
-                xvfb_proc = subprocess.Popen(xvfb_cmd,
-                                             stdout=open(os.devnull),
-                                             stderr=open(os.devnull))
-                time.sleep(0.2)  # give Xvfb time to start
-                if xvfb_proc.poll() is not None:
-                    raise Exception('Error: Xvfb did not start')
-                old_displaynum = os.environ['DISPLAY']
-                runtime.environ['DISPLAY'] = ':%s' % vdisplay_num
+                exist_val, _ = self._exists_in_path('Xvfb',
+                                                    runtime.environ)
+                if not exist_val:
+                    raise IOError("Xvfb could not be found on host %s" %
+                                  (runtime.hostname))
+                else:
+                    vdisplay_num = _search_for_free_display()
+                    xvfb_cmd = ['Xvfb', ':%d' % vdisplay_num]
+                    xvfb_proc = subprocess.Popen(xvfb_cmd,
+                                                 stdout=open(os.devnull),
+                                                 stderr=open(os.devnull))
+                    time.sleep(0.2)  # give Xvfb time to start
+                    if xvfb_proc.poll() is not None:
+                        raise Exception('Error: Xvfb did not start')
+                    old_displaynum = os.environ['DISPLAY']
+                    runtime.environ['DISPLAY'] = ':%s' % vdisplay_num
 
             runtime = self._run_interface(runtime)