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fixed fsl.Level1Design gamma convoluion #1500

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Merged
merged 6 commits into from
Jun 13, 2016
Merged

fixed fsl.Level1Design gamma convoluion #1500

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f28665b
enabled dgamma convolution
TheChymera Jun 8, 2016
79c71f1
notice of FSL Level1Design fix
TheChymera Jun 10, 2016
34c43e6
ev_none still needed for regressors
TheChymera Jun 10, 2016
d57a0c1
added test
TheChymera Jun 10, 2016
1b29133
removed superfluous import
TheChymera Jun 12, 2016
f75efb6
extended tests
TheChymera Jun 13, 2016
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1 change: 1 addition & 0 deletions CHANGES
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
Release 0.12.0-rc1 (April 20, 2016)
============

* FIX: Selecting "gamma" in FSL Level1Design now does what the name says (https://github.com/nipy/nipype/pull/1500)
* ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
* ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
* ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
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19 changes: 9 additions & 10 deletions nipype/interfaces/fsl/model.py
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Expand Up @@ -124,8 +124,8 @@ def _create_ev_file(self, evfname, evinfo):
f.close()

def _create_ev_files(
self, cwd, runinfo, runidx, usetd, contrasts, no_bases,
do_tempfilter):
self, cwd, runinfo, runidx, usetd, contrasts,
do_tempfilter, basis_key):
"""Creates EV files from condition and regressor information.

Parameters:
Expand All @@ -144,7 +144,9 @@ def _create_ev_files(
"""
conds = {}
evname = []
ev_hrf = load_template('feat_ev_hrf.tcl')
if basis_key == "dgamma":
basis_key = "hrf"
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ev_none is still needed for the regressors

ev_template = load_template('feat_ev_'+basis_key+'.tcl')
ev_none = load_template('feat_ev_none.tcl')
ev_ortho = load_template('feat_ev_ortho.tcl')
ev_txt = ''
Expand Down Expand Up @@ -174,13 +176,13 @@ def _create_ev_files(
evinfo.insert(j, [onset, cond['duration'][j], amp])
else:
evinfo.insert(j, [onset, cond['duration'][0], amp])
if no_bases:
ev_txt += ev_none.substitute(ev_num=num_evs[0],
if basis_key == "none":
ev_txt += ev_template.substitute(ev_num=num_evs[0],
ev_name=name,
tempfilt_yn=do_tempfilter,
cond_file=evfname)
else:
ev_txt += ev_hrf.substitute(ev_num=num_evs[0],
ev_txt += ev_template.substitute(ev_num=num_evs[0],
ev_name=name,
tempfilt_yn=do_tempfilter,
temporalderiv=usetd,
Expand Down Expand Up @@ -296,12 +298,9 @@ def _run_interface(self, runtime):
if isdefined(self.inputs.model_serial_correlations):
prewhiten = int(self.inputs.model_serial_correlations)
usetd = 0
no_bases = False
basis_key = list(self.inputs.bases.keys())[0]
if basis_key in ['dgamma', 'gamma']:
usetd = int(self.inputs.bases[basis_key]['derivs'])
if basis_key == 'none':
no_bases = True
session_info = self._format_session_info(self.inputs.session_info)
func_files = self._get_func_files(session_info)
n_tcon = 0
Expand All @@ -319,7 +318,7 @@ def _run_interface(self, runtime):
do_tempfilter = 0
num_evs, cond_txt = self._create_ev_files(cwd, info, i, usetd,
self.inputs.contrasts,
no_bases, do_tempfilter)
do_tempfilter, basis_key)
nim = load(func_files[i])
(_, _, _, timepoints) = nim.shape
fsf_txt = fsf_header.substitute(run_num=i,
Expand Down
20 changes: 20 additions & 0 deletions nipype/interfaces/fsl/tests/test_Level1Design.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
import os
from nose.tools import assert_true
from ...base import Undefined
from ..model import Level1Design

def test_level1design():
l = Level1Design()
runinfo = dict(cond=[{'name': 'test_condition', 'onset': [0, 10], 'duration':[10, 10]}],regress=[])
runidx = 0
contrasts = Undefined
usetd = False
do_tempfilter = False
output_num, output_txt = Level1Design._create_ev_files(l,os.getcwd(),runinfo,runidx,usetd,contrasts,do_tempfilter,"hrf")
yield assert_true, "set fmri(convolve1) 3" in output_txt
output_num, output_txt = Level1Design._create_ev_files(l,os.getcwd(),runinfo,runidx,usetd,contrasts,do_tempfilter,"dgamma")
yield assert_true, "set fmri(convolve1) 3" in output_txt
output_num, output_txt = Level1Design._create_ev_files(l,os.getcwd(),runinfo,runidx,usetd,contrasts,do_tempfilter,"gamma")
yield assert_true, "set fmri(convolve1) 2" in output_txt
output_num, output_txt = Level1Design._create_ev_files(l,os.getcwd(),runinfo,runidx,usetd,contrasts,do_tempfilter,"none")
yield assert_true, "set fmri(convolve1) 0" in output_txt