Merge pull request #1826 from TheChymera/flobs

aded support for custom IRF in FSL models

Author: satra

nipype/interfaces/fsl/model.py

@@ -42,6 +42,7 @@ class Level1DesignInputSpec(BaseInterfaceInputSpec):
             'dgamma'), traits.Dict(traits.Enum('derivs'), traits.Bool)),
         traits.Dict(traits.Enum('gamma'), traits.Dict(
                     traits.Enum('derivs', 'gammasigma', 'gammadelay'))),
+        traits.Dict(traits.Enum('custom'), traits.Dict(traits.Dict(traits.Enum('bfcustompath'), traits.Str))),
         traits.Dict(traits.Enum('none'), traits.Dict()),
         traits.Dict(traits.Enum('none'), traits.Enum(None)),
         mandatory=True,
@@ -192,10 +193,21 @@ def _create_ev_files(
                             evinfo.insert(j, [onset, cond['duration'][j], amp])
                         else:
                             evinfo.insert(j, [onset, cond['duration'][0], amp])
+                    ev_parameters['cond_file'] = evfname
                     ev_parameters['ev_num'] = num_evs[0]
                     ev_parameters['ev_name'] = name
                     ev_parameters['tempfilt_yn'] = do_tempfilter
-                    ev_parameters['cond_file'] = evfname
+                    if not 'basisorth' in ev_parameters:
+                        ev_parameters['basisorth'] = 1
+                    if not 'basisfnum' in ev_parameters:
+                        ev_parameters['basisfnum'] = 1
+                    try:
+                        ev_parameters['fsldir'] = os.environ['FSLDIR']
+                    except KeyError:
+                        if basis_key == 'flobs':
+                            raise Exception('FSL environment variables not set')
+                        else:
+                            ev_parameters['fsldir'] = '/usr/share/fsl'
                     try:
                         ev_parameters['temporalderiv'] = int(bool(ev_parameters.pop('derivs')))
                     except KeyError:

nipype/interfaces/fsl/tests/test_Level1Design_functions.py

@@ -12,8 +12,15 @@ def test_level1design():
     contrasts = Undefined
     do_tempfilter = False
     orthogonalization = {}
-    ev_parameters = {"temporalderiv":False}
-    for key, val in [('hrf', 3), ('dgamma', 3), ('gamma', 2), ('none', 0)]:
+    basic_ev_parameters = {'temporalderiv':False}
+    convolution_variants = [
+        ('custom', 7, {'temporalderiv':False, 'bfcustompath':'/some/path'}),
+        ('hrf', 3, basic_ev_parameters),
+        ('dgamma', 3, basic_ev_parameters),
+        ('gamma', 2, basic_ev_parameters),
+        ('none', 0, basic_ev_parameters)
+        ]
+    for key, val, ev_parameters in convolution_variants:
         output_num, output_txt = Level1Design._create_ev_files(l, os.getcwd(),
                                                                runinfo, runidx,
                                                                ev_parameters,

nipype/interfaces/script_templates/feat_ev_custom.tcl

@@ -0,0 +1,40 @@
+# EV title
+set fmri(evtitle$ev_num) "$ev_name"
+
+# Basic waveform shape (EV $ev_num)
+# 0 : Square
+# 1 : Sinusoid
+# 2 : Custom (1 entry per volume)
+# 3 : Custom (3 column format)
+# 4 : Interaction
+# 10 : Empty (all zeros)
+set fmri(shape$ev_num) 3
+
+# Convolution (EV $ev_num)
+# 0 : None
+# 1 : Gaussian
+# 2 : Gamma
+# 3 : Double-Gamma HRF
+# 4 : Gamma basis functions
+# 5 : Sine basis functions
+# 6 : FIR basis functions
+# 7 : Optimal/custom basis functions
+set fmri(convolve$ev_num) 7
+
+# Convolve phase (EV $ev_num)
+set fmri(convolve_phase$ev_num) 0
+
+# Apply temporal filtering (EV $ev_num)
+set fmri(tempfilt_yn$ev_num) $tempfilt_yn
+
+# Add temporal derivative (EV $ev_num)
+set fmri(deriv_yn$ev_num) $temporalderiv
+
+# Custom EV file (EV $ev_num)
+set fmri(custom$ev_num) "$cond_file"
+
+# Optimal/custom HRF convolution file
+set fmri(default_bfcustom) "${fsldir}/etc/default_flobs.flobs/hrfbasisfns.txt"
+set fmri(basisorth$ev_num) $basisorth
+set fmri(basisfnum$ev_num) $basisfnum
+set fmri(bfcustom) "$bfcustompath"

nipype/interfaces/script_templates/feat_ev_gamma.tcl

@@ -18,6 +18,7 @@ set fmri(shape$ev_num) 3
 # 4 : Gamma basis functions
 # 5 : Sine basis functions
 # 6 : FIR basis functions
+# 7 : Optimal/custom basis functions
 set fmri(convolve$ev_num) 2
 
 # Convolve phase

nipype/interfaces/script_templates/feat_ev_hrf.tcl

@@ -18,6 +18,7 @@ set fmri(shape$ev_num) 3
 # 4 : Gamma basis functions
 # 5 : Sine basis functions
 # 6 : FIR basis functions
+# 7 : Optimal/custom basis functions
 set fmri(convolve$ev_num) 3
 
 # Convolve phase (EV $ev_num)

nipype/interfaces/script_templates/feat_ev_none.tcl

@@ -18,6 +18,7 @@ set fmri(shape$ev_num) 2
 # 4 : Gamma basis functions
 # 5 : Sine basis functions
 # 6 : FIR basis functions
+# 7 : Optimal/custom basis functions
 set fmri(convolve$ev_num) 0
 
 # Apply temporal filtering