def main(arglist):
# Process cmdline args
parser = tools.parser
parser.description = help
parser.formatter_class = argparse.RawDescriptionHelpFormatter
args = tools.parser.parse_args(arglist)
plugin, plugin_args = lyman.determine_engine(args)
# Load up the lyman info
subject_list = lyman.determine_subjects(args.subjects)
project = lyman.gather_project_info()
# Create the workflow object
method = project["normalization"]
wf_func = getattr(anatwarp, "create_{}_workflow".format(method))
normalize = wf_func(project["data_dir"], subject_list)
normalize.base_dir = os.path.join(project["working_dir"], "warp")
# Put crashdumps somewhere out of the way
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
# Execute the workflow
lyman.run_workflow(normalize, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(normalize.base_dir)
def get_subject_order(exp):
subjects = lyman.determine_subjects([exp + "_subjects"])
accs = pd.Series(index=subjects, dtype=np.float)
for subj in subjects:
fname = "decoding_analysis/{}_{}_ifs.pkz".format(subj, exp)
accs.ix[subj] = moss.load_pkl(fname).acc
return list(accs.sort(inplace=False, ascending=False).index)
def main(arglist):
# Parse the command line
args = parse_args(arglist)
# Load the lyman data
subjects = lyman.determine_subjects(args.subjects)
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel)
contrasts = exp["contrast_names"]
z_thresh = exp["cluster_zthresh"]
# Get the full correct name for the experiment
if args.experiment is None:
exp_name = project["default_exp"]
else:
exp_name = args.experiment
exp_base = exp_name
if args.altmodel is not None:
exp_name = "-".join([exp_base, args.altmodel])
# Group-level
# ===========
if args.level == "group":
temp_base = op.join(project["analysis_dir"], exp_name, args.output,
args.regspace, "{contrast}")
if args.regspace == "fsaverage":
sig_thresh = -np.log10(stats.norm.sf(z_thresh))
sig_thresh = np.round(sig_thresh) * 10
corr_sign = exp["surf_corr_sign"]
sig_name = "cache.th%d.%s.sig.masked.mgh" % (sig_thresh, corr_sign)
stat_temp = op.join(temp_base, "{hemi}/osgm", sig_name)
mask_temp = op.join(temp_base, "{hemi}/mask.mgh")
png_temp = op.join(temp_base, "{hemi}/osgm/zstat_threshold.png")
else:
stat_temp = op.join(temp_base, "{hemi}.zstat1_threshold.mgz")
mask_temp = op.join(temp_base, "{hemi}.group_mask.mgz")
png_temp = op.join(temp_base, "zstat1_threshold_surf.png")
corr_sign = "pos"
contrast_loop("fsaverage", contrasts, stat_temp, mask_temp, png_temp,
args, z_thresh, corr_sign)
# Subject-level
# =============
elif args.level == "subject":
temp_base = op.join(project["analysis_dir"], exp_name, "{subj}", "ffx",
args.regspace, "smoothed/{contrast}")
mask_temp = op.join(temp_base, "{hemi}.mask.mgz")
stat_temp = op.join(temp_base, "{hemi}.zstat1.mgz")
png_temp = op.join(temp_base, "zstat1_surf.png")
for subj in subjects:
contrast_loop(subj, contrasts, stat_temp, mask_temp, png_temp,
args, 1.96, "abs")
def main(arglist):
# Parse the command line
args = parse_args(arglist)
# Load the lyman data
subjects = lyman.determine_subjects(args.subjects)
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel)
contrasts = exp["contrast_names"]
z_thresh = exp["cluster_zthresh"]
# Get the full correct name for the experiment
if args.experiment is None:
exp_name = project["default_exp"]
else:
exp_name = args.experiment
exp_base = exp_name
if args.altmodel is not None:
exp_name = "-".join([exp_base, args.altmodel])
# Group-level
# ===========
if args.level == "group":
temp_base = op.join(project["analysis_dir"], exp_name, args.output,
args.regspace, "{contrast}")
if args.regspace == "fsaverage":
sig_thresh = -np.log10(stats.norm.sf(z_thresh))
sig_thresh = np.round(sig_thresh) * 10
corr_sign = exp["surf_corr_sign"]
sig_name = "cache.th%d.%s.sig.masked.mgh" % (sig_thresh, corr_sign)
stat_temp = op.join(temp_base, "{hemi}/osgm", sig_name)
mask_temp = op.join(temp_base, "{hemi}/mask.mgh")
png_temp = op.join(temp_base, "{hemi}/osgm/zstat_threshold.png")
else:
stat_temp = op.join(temp_base, "{hemi}.zstat1_threshold.mgz")
mask_temp = op.join(temp_base, "{hemi}.group_mask.mgz")
png_temp = op.join(temp_base, "zstat1_threshold_surf.png")
corr_sign = "pos"
contrast_loop("fsaverage", contrasts, stat_temp, mask_temp, png_temp,
args, z_thresh, corr_sign)
# Subject-level
# =============
elif args.level == "subject":
temp_base = op.join(project["analysis_dir"], exp_name, "{subj}",
"ffx", args.regspace, "smoothed/{contrast}")
mask_temp = op.join(temp_base, "{hemi}.mask.mgz")
stat_temp = op.join(temp_base, "{hemi}.zstat1.mgz")
png_temp = op.join(temp_base, "zstat1_surf.png")
for subj in subjects:
contrast_loop(subj, contrasts, stat_temp, mask_temp, png_temp,
args, 1.96, "abs")
def main(arglist):
args = parse_args(arglist)
if args.subjects is None:
args.subjects = lyman.determine_subjects()
for subj in args.subjects:
print "Running subject", subj
searchlight_dir = op.join(analysis_dir, "dksort", subj,
"mvpa/searchlight")
if not op.exists(searchlight_dir):
os.mkdir(searchlight_dir)
vol_fname = op.join(searchlight_dir, "dimension_dksort_pfc.nii.gz")
if "fit" in args.do and (not op.exists(vol_fname) or args.overwrite):
print " Doing searchlight"
mask_img, X, y, runs = load_data(subj)
s = SearchLight(mask_img,
radius=10,
n_jobs=10,
estimator=LogisticRegression(),
cv=LeaveOneLabelOut(runs))
s.fit(X, y)
out_img = nib.Nifti1Image(s.scores_, s.mask_img.get_affine())
out_img.to_filename(vol_fname)
surf_fnames = [
op.join(searchlight_dir, "lh.dimension_dksort_pfc.mgz"),
op.join(searchlight_dir, "rh.dimension_dksort_pfc.mgz")
]
if "surf" in args.do and (not all(map(op.exists, surf_fnames))
or args.overwrite):
print " Doing surfreg"
reg_fname = op.join(analysis_dir, "dksort", subj,
"preproc/run_1/func2anat_tkreg.dat")
for i, hemi in enumerate(["lh", "rh"]):
cmdline = [
"mri_vol2surf", "--mov", vol_fname, "--reg", reg_fname,
"--trgsubject", "fsaverage", "--projfrac-avg", "0", "1",
".1", "--surf-fwhm", "5", "--hemi", hemi, "--o",
surf_fnames[i]
]
sp.check_output(" ".join(cmdline), shell=True)
def main(arglist):
args = parse_args(arglist)
if args.subjects is None:
args.subjects = lyman.determine_subjects()
for subj in args.subjects:
print "Running subject", subj
searchlight_dir = op.join(analysis_dir, "dksort", subj,
"mvpa/searchlight")
if not op.exists(searchlight_dir):
os.mkdir(searchlight_dir)
vol_fname = op.join(searchlight_dir, "dimension_dksort_pfc.nii.gz")
if "fit" in args.do and (not op.exists(vol_fname) or args.overwrite):
print " Doing searchlight"
mask_img, X, y, runs = load_data(subj)
s = SearchLight(mask_img, radius=10, n_jobs=10,
estimator=LogisticRegression(),
cv=LeaveOneLabelOut(runs))
s.fit(X, y)
out_img = nib.Nifti1Image(s.scores_, s.mask_img.get_affine())
out_img.to_filename(vol_fname)
surf_fnames = [op.join(searchlight_dir, "lh.dimension_dksort_pfc.mgz"),
op.join(searchlight_dir, "rh.dimension_dksort_pfc.mgz")]
if "surf" in args.do and (not all(map(op.exists, surf_fnames))
or args.overwrite):
print " Doing surfreg"
reg_fname = op.join(analysis_dir, "dksort", subj,
"preproc/run_1/func2anat_tkreg.dat")
for i, hemi in enumerate(["lh", "rh"]):
cmdline = ["mri_vol2surf",
"--mov", vol_fname,
"--reg", reg_fname,
"--trgsubject", "fsaverage",
"--projfrac-avg", "0", "1", ".1",
"--surf-fwhm", "5",
"--hemi", hemi,
"--o", surf_fnames[i]]
sp.check_output(" ".join(cmdline), shell=True)
def main(arglist):
# Find the subjects for this execution
args = parse_args(arglist)
subjects = lyman.determine_subjects(args.subjects)
# Find the project details
proj = lyman.gather_project_info()
data_dir = proj["data_dir"]
# Make images for each subject
for subj in subjects:
# Make sure the output directory exists
out_dir = op.join(data_dir, subj, "snapshots")
if not op.exists(out_dir):
os.mkdir(out_dir)
# Do each chunk of reporting
surface_images(out_dir, subj)
curvature_normalization(data_dir, subj)
volume_images(data_dir, subj)
def main(arglist):
# Process cmdline args
args = tools.parser.parse_args(arglist)
plugin, plugin_args = lyman.determine_engine(args)
# Load up the lyman info
subject_list = lyman.determine_subjects(args.subjects)
project = lyman.gather_project_info()
# Create the workflow object
normalize = anatwarp.create_anatwarp_workflow(
project["data_dir"], subject_list)
normalize.base_dir = project["working_dir"]
normalize.config["execution"]["crashdump_dir"] = "/tmp"
# Execute the workflow
lyman.run_workflow(normalize, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(normalize.base_dir)
def main(arglist):
# Find the subjects for this execution
args = parse_args(arglist)
subjects = lyman.determine_subjects(args.subjects)
# Find the project details
proj = lyman.gather_project_info()
data_dir = proj["data_dir"]
# Make images for each subject
for subj in subjects:
# Make sure the output directory exists
out_dir = op.join(data_dir, subj, "snapshots")
if not op.exists(out_dir):
os.mkdir(out_dir)
# Do each chunk of reporting
inflated_surfaces(out_dir, subj, args.close)
curvature_normalization(data_dir, subj, args.close)
volume_images(data_dir, subj)
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel)
# Set up the SUBJECTS_DIR for Freesurfer
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Subject is always highest level of parameterization
subject_list = lyman.determine_subjects(args.subjects)
subj_source = tools.make_subject_source(subject_list)
# Get the full correct name for the experiment
if args.experiment is None:
exp_name = project["default_exp"]
else:
exp_name = args.experiment
exp_base = exp_name
if args.altmodel is not None:
exp_name = "-".join([exp_base, args.altmodel])
# Set roots of output storage
data_dir = project["data_dir"]
analysis_dir = op.join(project["analysis_dir"], exp_name)
working_dir = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
# Create symlinks to the preproc directory for altmodels
if not op.exists(analysis_dir):
os.makedirs(analysis_dir)
if exp_base != exp_name:
for subj in subject_list:
subj_dir = op.join(analysis_dir, subj)
if not op.exists(subj_dir):
os.makedirs(subj_dir)
link_dir = op.join(analysis_dir, subj, "preproc")
if not op.exists(link_dir):
preproc_dir = op.join("../..", exp_base, subj, "preproc")
os.symlink(preproc_dir, link_dir)
# For later processing steps, are we using smoothed inputs?
smoothing = "unsmoothed" if args.unsmoothed else "smoothed"
# Also define the regspace variable here
space = args.regspace
# ----------------------------------------------------------------------- #
# Preprocessing Workflow
# ----------------------------------------------------------------------- #
# Create workflow in function defined elsewhere in this package
preproc, preproc_input, preproc_output = wf.create_preprocessing_workflow(
exp_info=exp)
# Collect raw nifti data
preproc_templates = dict(timeseries=exp["source_template"])
if exp["partial_brain"]:
preproc_templates["whole_brain_template"] = exp["whole_brain_template"]
preproc_source = Node(SelectFiles(preproc_templates,
base_directory=project["data_dir"]),
"preproc_source")
# Convenience class to handle some sterotyped connections
# between run-specific nodes (defined here) and the inputs
# to the prepackaged workflow returned above
preproc_inwrap = tools.InputWrapper(preproc, subj_source,
preproc_source, preproc_input)
preproc_inwrap.connect_inputs()
# Store workflow outputs to persistant location
preproc_sink = Node(DataSink(base_directory=analysis_dir), "preproc_sink")
# Similar to above, class to handle sterotyped output connections
preproc_outwrap = tools.OutputWrapper(preproc, subj_source,
preproc_sink, preproc_output)
preproc_outwrap.set_subject_container()
preproc_outwrap.set_mapnode_substitutions(exp["n_runs"])
preproc_outwrap.sink_outputs("preproc")
# Set the base for the possibly temporary working directory
preproc.base_dir = working_dir
# Possibly execute the workflow, depending on the command line
lyman.run_workflow(preproc, "preproc", args)
# ----------------------------------------------------------------------- #
# Timeseries Model
# ----------------------------------------------------------------------- #
# Create a modelfitting workflow and specific nodes as above
model, model_input, model_output = wf.create_timeseries_model_workflow(
name=smoothing + "_model", exp_info=exp)
model_base = op.join(analysis_dir, "{subject_id}/preproc/run_*/")
model_templates = dict(
timeseries=op.join(model_base, smoothing + "_timeseries.nii.gz"),
realign_file=op.join(model_base, "realignment_params.csv"),
artifact_file=op.join(model_base, "artifacts.csv"),
)
if exp["design_name"] is not None:
design_file = exp["design_name"] + ".csv"
regressor_file = exp["design_name"] + ".csv"
model_templates["design_file"] = op.join(data_dir, "{subject_id}",
"design", design_file)
if exp["regressor_file"] is not None:
regressor_file = exp["regressor_file"] + ".csv"
model_templates["regressor_file"] = op.join(data_dir, "{subject_id}",
"design", regressor_file)
model_source = Node(SelectFiles(model_templates), "model_source")
model_inwrap = tools.InputWrapper(model, subj_source,
model_source, model_input)
model_inwrap.connect_inputs()
model_sink = Node(DataSink(base_directory=analysis_dir), "model_sink")
model_outwrap = tools.OutputWrapper(model, subj_source,
model_sink, model_output)
model_outwrap.set_subject_container()
model_outwrap.set_mapnode_substitutions(exp["n_runs"])
model_outwrap.sink_outputs("model." + smoothing)
# Set temporary output locations
model.base_dir = working_dir
# Possibly execute the workflow
lyman.run_workflow(model, "model", args)
# ----------------------------------------------------------------------- #
# Across-Run Registration
# ----------------------------------------------------------------------- #
# Is this a model or timeseries registration?
regtype = "timeseries" if (args.timeseries or args.residual) else "model"
# Retrieve the right workflow function for registration
# Get the workflow function dynamically based on the space
warp_method = project["normalization"]
flow_name = "%s_%s_reg" % (space, regtype)
reg, reg_input, reg_output = wf.create_reg_workflow(flow_name,
space,
regtype,
warp_method,
args.residual)
# Define a smoothing info node here. Use an iterable so that running
# with/without smoothing doesn't clobber working directory files
# for the other kind of execution
smooth_source = Node(IdentityInterface(fields=["smoothing"]),
iterables=("smoothing", [smoothing]),
name="smooth_source")
# Set up the registration inputs and templates
reg_templates = dict(
masks="{subject_id}/preproc/run_*/functional_mask.nii.gz",
means="{subject_id}/preproc/run_*/mean_func.nii.gz",
)
if regtype == "model":
reg_base = "{subject_id}/model/{smoothing}/run_*/"
reg_templates.update(dict(
copes=op.join(reg_base, "cope*.nii.gz"),
varcopes=op.join(reg_base, "varcope*.nii.gz"),
sumsquares=op.join(reg_base, "ss*.nii.gz"),
))
else:
if args.residual:
ts_file = op.join("{subject_id}/model/{smoothing}/run_*/",
"results/res4d.nii.gz")
else:
ts_file = op.join("{subject_id}/preproc/run_*/",
"{smoothing}_timeseries.nii.gz")
reg_templates.update(dict(timeseries=ts_file))
reg_lists = reg_templates.keys()
if space == "mni":
aff_ext = "mat" if warp_method == "fsl" else "txt"
reg_templates["warpfield"] = op.join(data_dir, "{subject_id}",
"normalization/warpfield.nii.gz")
reg_templates["affine"] = op.join(data_dir, "{subject_id}",
"normalization/affine." + aff_ext)
rigid_stem = "{subject_id}/preproc/run_*/func2anat_"
if warp_method == "ants" and space == "mni":
reg_templates["rigids"] = rigid_stem + "tkreg.dat"
else:
reg_templates["rigids"] = rigid_stem + "flirt.mat"
# Define the registration data source node
reg_source = Node(SelectFiles(reg_templates,
force_lists=reg_lists,
base_directory=analysis_dir),
"reg_source")
# Registration inputnode
reg_inwrap = tools.InputWrapper(reg, subj_source,
reg_source, reg_input)
reg_inwrap.connect_inputs()
# The source node also needs to know about the smoothing on this run
reg.connect(smooth_source, "smoothing", reg_source, "smoothing")
# Set up the registration output and datasink
reg_sink = Node(DataSink(base_directory=analysis_dir), "reg_sink")
reg_outwrap = tools.OutputWrapper(reg, subj_source,
reg_sink, reg_output)
reg_outwrap.set_subject_container()
reg_outwrap.sink_outputs("reg.%s" % space)
# Reg has some additional substitutions to strip out iterables
# and rename the timeseries file
reg_subs = [("_smoothing_", "")]
reg_outwrap.add_regexp_substitutions(reg_subs)
# Add dummy substitutions for the contasts to make sure the DataSink
# reruns when the deisgn has changed. This accounts for the problem where
# directory inputs are treated as strings and the contents/timestamps are
# not hashed, which should be fixed upstream soon.
contrast_subs = [(c, c) for c in exp["contrast_names"]]
reg_outwrap.add_regexp_substitutions(contrast_subs)
reg.base_dir = working_dir
# Possibly run registration workflow and clean up
lyman.run_workflow(reg, "reg", args)
# ----------------------------------------------------------------------- #
# Across-Run Fixed Effects Model
# ----------------------------------------------------------------------- #
# Dynamically get the workflow
wf_name = space + "_ffx"
ffx, ffx_input, ffx_output = wf.create_ffx_workflow(wf_name,
space,
exp["contrast_names"])
ext = "_warp.nii.gz" if space == "mni" else "_xfm.nii.gz"
ffx_base = op.join("{subject_id}/reg", space, "{smoothing}/run_*")
ffx_templates = dict(
copes=op.join(ffx_base, "cope*" + ext),
varcopes=op.join(ffx_base, "varcope*" + ext),
masks=op.join(ffx_base, "functional_mask" + ext),
means=op.join(ffx_base, "mean_func" + ext),
dofs="{subject_id}/model/{smoothing}/run_*/results/dof",
ss_files=op.join(ffx_base, "ss*" + ext),
timeseries="{subject_id}/preproc/run_*/{smoothing}_timeseries.nii.gz",
)
ffx_lists = ffx_templates.keys()
# Space-conditional inputs
if space == "mni":
bg = op.join(data_dir, "{subject_id}/normalization/brain_warp.nii.gz")
reg = op.join(os.environ["FREESURFER_HOME"],
"average/mni152.register.dat")
else:
bg = "{subject_id}/preproc/run_1/mean_func.nii.gz"
reg = "{subject_id}/preproc/run_1/func2anat_tkreg.dat"
ffx_templates["anatomy"] = bg
ffx_templates["reg_file"] = reg
# Define the ffxistration data source node
ffx_source = Node(SelectFiles(ffx_templates,
force_lists=ffx_lists,
base_directory=analysis_dir),
"ffx_source")
# Fixed effects inutnode
ffx_inwrap = tools.InputWrapper(ffx, subj_source,
ffx_source, ffx_input)
ffx_inwrap.connect_inputs()
# Connect the smoothing information
ffx.connect(smooth_source, "smoothing", ffx_source, "smoothing")
# Fixed effects output and datasink
ffx_sink = Node(DataSink(base_directory=analysis_dir), "ffx_sink")
ffx_outwrap = tools.OutputWrapper(ffx, subj_source,
ffx_sink, ffx_output)
ffx_outwrap.set_subject_container()
ffx_outwrap.sink_outputs("ffx.%s" % space)
# Fixed effects has some additional substitutions to strip out interables
ffx_outwrap.add_regexp_substitutions([
("_smoothing_", ""), ("flamestats", "")
])
ffx.base_dir = working_dir
# Possibly run fixed effects workflow
lyman.run_workflow(ffx, "ffx", args)
# -------- #
# Clean-up
# -------- #
if project["rm_working_dir"]:
shutil.rmtree(project["working_dir"])
import numpy as np
import pandas as pd
from scipy import stats, signal
import statsmodels.api as sm
import nibabel as nib
import seaborn as sns
import matplotlib.pyplot as plt
from surfer import Brain
import moss
from moss import glm
from moss.nipy import VolumeImg
import lyman
subjects = lyman.determine_subjects()
project = lyman.gather_project_info()
data_dir = project["data_dir"]
analysis_dir = project["analysis_dir"]
exp = project["default_exp"]
design_temp = op.join(data_dir, "{}/design/{}.csv")
class SlicePlotter(object):
"""Object to generate single slice images or mosaics of volume results."""
def __init__(self,
model,
contrast,
corrected=True,
stat_thresh=2.3,
stat_range=(2, 5),
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel, args)
# Set up the SUBJECTS_DIR for Freesurfer
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Subject is always highest level of parameterization
subject_list = lyman.determine_subjects(args.subjects)
subj_source = tools.make_subject_source(subject_list)
# Get the full correct name for the experiment
if args.experiment is None:
exp_name = project["default_exp"]
else:
exp_name = args.experiment
exp_base = exp_name
if args.altmodel is not None:
exp_name = "-".join([exp_base, args.altmodel])
# Set roots of output storage
data_dir = project["data_dir"]
analysis_dir = op.join(project["analysis_dir"], exp_name)
working_dir = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
# Create symlinks to the preproc directory for altmodels
if not op.exists(analysis_dir):
os.makedirs(analysis_dir)
if exp_base != exp_name:
for subj in subject_list:
subj_dir = op.join(analysis_dir, subj)
if not op.exists(subj_dir):
os.makedirs(subj_dir)
link_dir = op.join(analysis_dir, subj, "preproc")
if not op.exists(link_dir):
preproc_dir = op.join("../..", exp_base, subj, "preproc")
os.symlink(preproc_dir, link_dir)
# For later processing steps, are we using smoothed inputs?
smoothing = "unsmoothed" if args.unsmoothed else "smoothed"
# Also define the regspace variable here
space = args.regspace
# ----------------------------------------------------------------------- #
# Preprocessing Workflow
# ----------------------------------------------------------------------- #
# Create workflow in function defined elsewhere in this package
preproc, preproc_input, preproc_output = wf.create_preprocessing_workflow(
exp_info=exp)
# Collect raw nifti data
preproc_templates = dict(timeseries=exp["source_template"])
if exp["partial_brain"]:
preproc_templates["whole_brain"] = exp["whole_brain_template"]
if exp["fieldmap_template"]:
preproc_templates["fieldmap"] = exp["fieldmap_template"]
preproc_source = Node(
SelectFiles(preproc_templates, base_directory=project["data_dir"]),
"preproc_source")
# Convenience class to handle some sterotyped connections
# between run-specific nodes (defined here) and the inputs
# to the prepackaged workflow returned above
preproc_inwrap = tools.InputWrapper(preproc, subj_source, preproc_source,
preproc_input)
preproc_inwrap.connect_inputs()
# Store workflow outputs to persistant location
preproc_sink = Node(DataSink(base_directory=analysis_dir), "preproc_sink")
# Similar to above, class to handle sterotyped output connections
preproc_outwrap = tools.OutputWrapper(preproc, subj_source, preproc_sink,
preproc_output)
preproc_outwrap.set_subject_container()
preproc_outwrap.set_mapnode_substitutions(exp["n_runs"])
preproc_outwrap.sink_outputs("preproc")
# Set the base for the possibly temporary working directory
preproc.base_dir = working_dir
# Possibly execute the workflow, depending on the command line
lyman.run_workflow(preproc, "preproc", args)
# ----------------------------------------------------------------------- #
# Timeseries Model
# ----------------------------------------------------------------------- #
# Create a modelfitting workflow and specific nodes as above
model, model_input, model_output = wf.create_timeseries_model_workflow(
name=smoothing + "_model", exp_info=exp)
model_base = op.join(analysis_dir, "{subject_id}/preproc/run_*/")
model_templates = dict(
timeseries=op.join(model_base, smoothing + "_timeseries.nii.gz"),
realign_file=op.join(model_base, "realignment_params.csv"),
nuisance_file=op.join(model_base, "nuisance_variables.csv"),
artifact_file=op.join(model_base, "artifacts.csv"),
)
if exp["design_name"] is not None:
design_file = exp["design_name"] + ".csv"
regressor_file = exp["design_name"] + ".csv"
model_templates["design_file"] = op.join(data_dir, "{subject_id}",
"design", design_file)
if exp["regressor_file"] is not None:
regressor_file = exp["regressor_file"] + ".csv"
model_templates["regressor_file"] = op.join(data_dir, "{subject_id}",
"design", regressor_file)
model_source = Node(SelectFiles(model_templates), "model_source")
model_inwrap = tools.InputWrapper(model, subj_source, model_source,
model_input)
model_inwrap.connect_inputs()
model_sink = Node(DataSink(base_directory=analysis_dir), "model_sink")
model_outwrap = tools.OutputWrapper(model, subj_source, model_sink,
model_output)
model_outwrap.set_subject_container()
model_outwrap.set_mapnode_substitutions(exp["n_runs"])
model_outwrap.sink_outputs("model." + smoothing)
# Set temporary output locations
model.base_dir = working_dir
# Possibly execute the workflow
lyman.run_workflow(model, "model", args)
# ----------------------------------------------------------------------- #
# Across-Run Registration
# ----------------------------------------------------------------------- #
# Is this a model or timeseries registration?
regtype = "timeseries" if (args.timeseries or args.residual) else "model"
# Are we registering across experiments?
cross_exp = args.regexp is not None
# Retrieve the right workflow function for registration
# Get the workflow function dynamically based on the space
warp_method = project["normalization"]
flow_name = "%s_%s_reg" % (space, regtype)
reg, reg_input, reg_output = wf.create_reg_workflow(
flow_name, space, regtype, warp_method, args.residual, cross_exp)
# Define a smoothing info node here. Use an iterable so that running
# with/without smoothing doesn't clobber working directory files
# for the other kind of execution
smooth_source = Node(IdentityInterface(fields=["smoothing"]),
iterables=("smoothing", [smoothing]),
name="smooth_source")
# Set up the registration inputs and templates
reg_templates = dict(
masks="{subject_id}/preproc/run_*/functional_mask.nii.gz",
means="{subject_id}/preproc/run_*/mean_func.nii.gz",
)
if regtype == "model":
# First-level model summary statistic images
reg_base = "{subject_id}/model/{smoothing}/run_*/"
reg_templates.update(
dict(
copes=op.join(reg_base, "cope*.nii.gz"),
varcopes=op.join(reg_base, "varcope*.nii.gz"),
sumsquares=op.join(reg_base, "ss*.nii.gz"),
))
else:
# Timeseries images
if args.residual:
ts_file = op.join("{subject_id}/model/{smoothing}/run_*/",
"results/res4d.nii.gz")
else:
ts_file = op.join("{subject_id}/preproc/run_*/",
"{smoothing}_timeseries.nii.gz")
reg_templates.update(dict(timeseries=ts_file))
reg_lists = list(reg_templates.keys())
# Native anatomy to group anatomy affine matrix and warpfield
if space == "mni":
aff_ext = "mat" if warp_method == "fsl" else "txt"
reg_templates["warpfield"] = op.join(data_dir, "{subject_id}",
"normalization/warpfield.nii.gz")
reg_templates["affine"] = op.join(data_dir, "{subject_id}",
"normalization/affine." + aff_ext)
else:
if args.regexp is None:
tkreg_base = analysis_dir
else:
tkreg_base = op.join(project["analysis_dir"], args.regexp)
reg_templates["tkreg_rigid"] = op.join(tkreg_base, "{subject_id}",
"preproc", "run_1",
"func2anat_tkreg.dat")
# Rigid (6dof) functional-to-anatomical matrices
rigid_stem = "{subject_id}/preproc/run_*/func2anat_"
if warp_method == "ants" and space == "mni":
reg_templates["rigids"] = rigid_stem + "tkreg.dat"
else:
reg_templates["rigids"] = rigid_stem + "flirt.mat"
# Rigid matrix from anatomy to target experiment space
if args.regexp is not None:
targ_analysis_dir = op.join(project["analysis_dir"], args.regexp)
reg_templates["first_rigid"] = op.join(targ_analysis_dir,
"{subject_id}", "preproc",
"run_1", "func2anat_flirt.mat")
# Define the registration data source node
reg_source = Node(
SelectFiles(reg_templates,
force_lists=reg_lists,
base_directory=analysis_dir), "reg_source")
# Registration inputnode
reg_inwrap = tools.InputWrapper(reg, subj_source, reg_source, reg_input)
reg_inwrap.connect_inputs()
# The source node also needs to know about the smoothing on this run
reg.connect(smooth_source, "smoothing", reg_source, "smoothing")
# Set up the registration output and datasink
reg_sink = Node(DataSink(base_directory=analysis_dir), "reg_sink")
reg_outwrap = tools.OutputWrapper(reg, subj_source, reg_sink, reg_output)
reg_outwrap.set_subject_container()
reg_outwrap.sink_outputs("reg.%s" % space)
# Reg has some additional substitutions to strip out iterables
# and rename the timeseries file
reg_subs = [("_smoothing_", "")]
reg_outwrap.add_regexp_substitutions(reg_subs)
# Add dummy substitutions for the contasts to make sure the DataSink
# reruns when the deisgn has changed. This accounts for the problem where
# directory inputs are treated as strings and the contents/timestamps are
# not hashed, which should be fixed upstream soon.
contrast_subs = [(c, c) for c in exp["contrast_names"]]
reg_outwrap.add_regexp_substitutions(contrast_subs)
reg.base_dir = working_dir
# Possibly run registration workflow and clean up
lyman.run_workflow(reg, "reg", args)
# ----------------------------------------------------------------------- #
# Across-Run Fixed Effects Model
# ----------------------------------------------------------------------- #
# Dynamically get the workflow
wf_name = space + "_ffx"
ffx, ffx_input, ffx_output = wf.create_ffx_workflow(wf_name,
space,
exp["contrast_names"],
exp_info=exp)
ext = "_warp.nii.gz" if space == "mni" else "_xfm.nii.gz"
ffx_base = op.join("{subject_id}/reg", space, "{smoothing}/run_*")
ffx_templates = dict(
copes=op.join(ffx_base, "cope*" + ext),
varcopes=op.join(ffx_base, "varcope*" + ext),
masks=op.join(ffx_base, "functional_mask" + ext),
means=op.join(ffx_base, "mean_func" + ext),
dofs="{subject_id}/model/{smoothing}/run_*/results/dof",
ss_files=op.join(ffx_base, "ss*" + ext),
timeseries="{subject_id}/preproc/run_*/{smoothing}_timeseries.nii.gz",
)
ffx_lists = list(ffx_templates.keys())
# Space-conditional inputs
if space == "mni":
bg = op.join(data_dir, "{subject_id}/normalization/brain_warp.nii.gz")
reg = op.join(os.environ["FREESURFER_HOME"],
"average/mni152.register.dat")
else:
reg_dir = "{subject_id}/reg/epi/{smoothing}/run_1"
bg = op.join(reg_dir, "mean_func_xfm.nii.gz")
reg = op.join(reg_dir, "func2anat_tkreg.dat")
ffx_templates["anatomy"] = bg
ffx_templates["reg_file"] = reg
# Define the ffxistration data source node
ffx_source = Node(
SelectFiles(ffx_templates,
force_lists=ffx_lists,
base_directory=analysis_dir), "ffx_source")
# Fixed effects inutnode
ffx_inwrap = tools.InputWrapper(ffx, subj_source, ffx_source, ffx_input)
ffx_inwrap.connect_inputs()
# Connect the smoothing information
ffx.connect(smooth_source, "smoothing", ffx_source, "smoothing")
# Fixed effects output and datasink
ffx_sink = Node(DataSink(base_directory=analysis_dir), "ffx_sink")
ffx_outwrap = tools.OutputWrapper(ffx, subj_source, ffx_sink, ffx_output)
ffx_outwrap.set_subject_container()
ffx_outwrap.sink_outputs("ffx.%s" % space)
# Fixed effects has some additional substitutions to strip out interables
ffx_outwrap.add_regexp_substitutions([("_smoothing_", ""),
("flamestats", "")])
ffx.base_dir = working_dir
# Possibly run fixed effects workflow
lyman.run_workflow(ffx, "ffx", args)
# -------- #
# Clean-up
# -------- #
if project["rm_working_dir"]:
shutil.rmtree(working_dir)
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel)
if args.experiment is None:
args.experiment = project["default_exp"]
if args.altmodel:
exp_name = "-".join([args.experiment, args.altmodel])
else:
exp_name = args.experiment
# Make sure some paths are set properly
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Set roots of output storage
anal_dir_base = op.join(project["analysis_dir"], exp_name)
work_dir_base = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
### Set up group info
## Regular design
group_info = pd.read_csv(group_filepath)
# Subject source (no iterables here)
subject_list = lyman.determine_subjects(args.subjects)
# Additional code (deletion caught by Dan dillon)
subj_source = Node(IdentityInterface(fields=["subject_id"]),
name="subj_source")
subj_source.inputs.subject_id = subject_list
print(group_info)
print(subject_list)
groups = [group_info[group_info.subid == x].reset_index().at[0,'group'] for x in subject_list]
group_vector = [1 if sub == "group1" else 2 for sub in groups] # 1 for group1, 2 for group2
# Set up the regressors and contrasts
regressors = dict(group1_mean=[int(sub == 'group1') for sub in groups],
group2_mean=[int(sub == 'group2') for sub in groups])
print(regressors)
# DECIDE WHICH CONTRAST YOU WANT HERE:
contrasts = [[contrast_name, "T", ["group1_mean", "group2_mean"], contrast_vals]]
print('Using this contrast:')
print(contrast_name)
print(contrast_vals)
# Subject level contrast source
contrast_source = Node(IdentityInterface(fields=["l1_contrast"]),
iterables=("l1_contrast", exp["contrast_names"]),
name="contrast_source")
# Group workflow
space = args.regspace
wf_name = "_".join([space, args.output])
if space == "mni":
mfx, mfx_input, mfx_output = wf.create_volume_mixedfx_workflow_groups(
wf_name, subject_list, regressors, contrasts, exp, group_vector)
else:
mfx, mfx_input, mfx_output = wf.create_surface_ols_workflow(
wf_name, subject_list, exp)
# Mixed effects inputs
ffxspace = "mni" if space == "mni" else "epi"
ffxsmooth = "unsmoothed" if args.unsmoothed else "smoothed"
mfx_base = op.join("{subject_id}/ffx/%s/%s/{l1_contrast}" % (ffxspace,
ffxsmooth))
templates = dict(copes=op.join(mfx_base, "cope1.nii.gz"))
if space == "mni":
templates.update(dict(
varcopes=op.join(mfx_base, "varcope1.nii.gz"),
dofs=op.join(mfx_base, "tdof_t1.nii.gz")))
else:
templates.update(dict(
reg_file=op.join(anal_dir_base, "{subject_id}/preproc/run_1",
"func2anat_tkreg.dat")))
# Workflow source node
mfx_source = MapNode(SelectFiles(templates,
base_directory=anal_dir_base,
sort_filelist=True),
"subject_id",
"mfx_source")
# Workflow input connections
mfx.connect([
(contrast_source, mfx_source,
[("l1_contrast", "l1_contrast")]),
(contrast_source, mfx_input,
[("l1_contrast", "l1_contrast")]),
(subj_source, mfx_source,
[("subject_id", "subject_id")]),
(mfx_source, mfx_input,
[("copes", "copes")])
]),
if space == "mni":
mfx.connect([
(mfx_source, mfx_input,
[("varcopes", "varcopes"),
("dofs", "dofs")]),
])
else:
mfx.connect([
(mfx_source, mfx_input,
[("reg_file", "reg_file")]),
(subj_source, mfx_input,
[("subject_id", "subject_id")])
])
# Mixed effects outputs
mfx_sink = Node(DataSink(base_directory="/".join([anal_dir_base,
args.output,
space]),
substitutions=[("/stats", "/"),
("/_hemi_", "/"),
("_glm_results", "")],
parameterization=True),
name="mfx_sink")
mfx_outwrap = tools.OutputWrapper(mfx, subj_source,
mfx_sink, mfx_output)
mfx_outwrap.sink_outputs()
mfx_outwrap.set_mapnode_substitutions(1)
mfx_outwrap.add_regexp_substitutions([
(r"_l1_contrast_[-\w]*/", "/"),
(r"_mni_hemi_[lr]h", "")
])
mfx.connect(contrast_source, "l1_contrast",
mfx_sink, "container")
# Set a few last things
mfx.base_dir = work_dir_base
# Execute
lyman.run_workflow(mfx, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(project["working_dir"])
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel)
if args.experiment is None:
args.experiment = project["default_exp"]
if args.altmodel:
exp_name = "-".join([args.experiment, args.altmodel])
else:
exp_name = args.experiment
# Make sure some paths are set properly
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Set roots of output storage
anal_dir_base = op.join(project["analysis_dir"], exp_name)
work_dir_base = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
### Set up group info
## Regular design
# Subject source (no iterables here)
subject_list = lyman.determine_subjects(args.subjects)
print subject_list
subj_source = Node(IdentityInterface(fields=["subject_id"]),
name="subj_source")
subj_source.inputs.subject_id = subject_list
# load in covariate for source accuracy analysis
# cov = pd.read_csv('/Volumes/group/awagner/sgagnon/AP/results/df_sourceAcc.csv')
# cov_col = 'mean_acc'
# load in covariate (subids and value for each subject (in cov_col))
cov = pd.read_csv(cov_filepath)
cov = cov.loc[cov.subid.isin(subject_list)] # prune for those in this analysis
cov[cov_col] = (cov[cov_col] - cov[cov_col].mean()) / cov[cov_col].std() # zscore
print cov.describe()
cov_reg = [cov[cov.subid == x].reset_index().at[0, cov_col] for x in subject_list]
# Set up the regressors and contrasts
regressors = dict(group_mean=[int(1) for sub in subject_list], z_covariate=cov_reg)
print regressors
contrasts = [["cov", "T", ["group_mean", "z_covariate"], [0, 1]]]
# Subject level contrast source
contrast_source = Node(IdentityInterface(fields=["l1_contrast"]),
iterables=("l1_contrast", exp["contrast_names"]),
name="contrast_source")
# Group workflow
space = args.regspace
wf_name = "_".join([space, args.output])
if space == "mni":
mfx, mfx_input, mfx_output = wf.create_volume_mixedfx_workflow(
wf_name, subject_list, regressors, contrasts, exp)
else:
print 'run mni!'
# Mixed effects inputs
ffxspace = "mni" if space == "mni" else "epi"
ffxsmooth = "unsmoothed" if args.unsmoothed else "smoothed"
mfx_base = op.join("{subject_id}/ffx/%s/%s/{l1_contrast}" % (ffxspace,
ffxsmooth))
templates = dict(copes=op.join(mfx_base, "cope1.nii.gz"))
if space == "mni":
templates.update(dict(
varcopes=op.join(mfx_base, "varcope1.nii.gz"),
dofs=op.join(mfx_base, "tdof_t1.nii.gz")))
else:
templates.update(dict(
reg_file=op.join(anal_dir_base, "{subject_id}/preproc/run_1",
"func2anat_tkreg.dat")))
# Workflow source node
mfx_source = MapNode(SelectFiles(templates,
base_directory=anal_dir_base,
sort_filelist=True),
"subject_id",
"mfx_source")
# Workflow input connections
mfx.connect([
(contrast_source, mfx_source,
[("l1_contrast", "l1_contrast")]),
(contrast_source, mfx_input,
[("l1_contrast", "l1_contrast")]),
(subj_source, mfx_source,
[("subject_id", "subject_id")]),
(mfx_source, mfx_input,
[("copes", "copes")])
]),
if space == "mni":
mfx.connect([
(mfx_source, mfx_input,
[("varcopes", "varcopes"),
("dofs", "dofs")]),
])
else:
mfx.connect([
(mfx_source, mfx_input,
[("reg_file", "reg_file")]),
(subj_source, mfx_input,
[("subject_id", "subject_id")])
])
# Mixed effects outputs
mfx_sink = Node(DataSink(base_directory="/".join([anal_dir_base,
args.output,
space]),
substitutions=[("/stats", "/"),
("/_hemi_", "/"),
("_glm_results", "")],
parameterization=True),
name="mfx_sink")
mfx_outwrap = tools.OutputWrapper(mfx, subj_source,
mfx_sink, mfx_output)
mfx_outwrap.sink_outputs()
mfx_outwrap.set_mapnode_substitutions(1)
mfx_outwrap.add_regexp_substitutions([
(r"_l1_contrast_[-\w]*/", "/"),
(r"_mni_hemi_[lr]h", "")
])
mfx.connect(contrast_source, "l1_contrast",
mfx_sink, "container")
# Set a few last things
mfx.base_dir = work_dir_base
# Execute
lyman.run_workflow(mfx, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(project["working_dir"])
import numpy as np
import pandas as pd
import moss
import lyman
if __name__ == "__main__":
subjects = dict(dots=lyman.determine_subjects(["dots_subjects"]),
sticks=lyman.determine_subjects(["sticks_subjects"]))
# ----- Combine decoding results
rois = ["ifs", "mfc"]
decoding_data = {}
for exp, subj_list in subjects.iteritems():
# Set up the dataframe for this experiment
idx = pd.MultiIndex.from_product([subj_list, rois],
names=["subj", "roi"])
exp_df = pd.DataFrame(index=idx,
columns=["acc", "chance", "pctile"],
dtype=np.float)
# Load the data for each subject/roi
for subj, roi in idx:
fname = "decoding_analysis/{}_{}_{}.pkz".format(subj, exp, roi)
res = moss.load_pkl(fname)
exp_df.ix[subj, roi] = [res.acc, res.chance, res.acc_pctile]
decoding_data[exp] = exp_df
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel)
if args.experiment is None:
args.experiment = project["default_exp"]
if args.altmodel:
exp_name = "-".join([args.experiment, args.altmodel])
else:
exp_name = args.experiment
# Make sure some paths are set properly
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Set roots of output storage
anal_dir_base = op.join(project["analysis_dir"], exp_name)
work_dir_base = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
### Set up group info
## Regular design
# Subject source (no iterables here)
subject_list = lyman.determine_subjects(args.subjects)
print subject_list
subj_source = Node(IdentityInterface(fields=["subject_id"]),
name="subj_source")
subj_source.inputs.subject_id = subject_list
# load in covariate for source accuracy analysis
# cov = pd.read_csv('/Volumes/group/awagner/sgagnon/AP/results/df_sourceAcc.csv')
# cov_col = 'mean_acc'
# load in covariate for cort analysis
cov = pd.read_csv(
'/Volumes/group/awagner/sgagnon/AP/data/cortisol/cort_percentchange_testbaseline_controlassay.csv'
)
cov_col = 'cort_controlassay'
cov = cov.loc[cov.subid.isin(
subject_list)] # prune for those in this analysis
cov[cov_col] = (cov[cov_col] -
cov[cov_col].mean()) / cov[cov_col].std() # zscore
print cov.describe()
cov_reg = [
cov[cov.subid == x].reset_index().at[0, cov_col] for x in subject_list
]
# Set up the regressors and contrasts
regressors = dict(group_mean=[int(1) for sub in subject_list],
z_covariate=cov_reg)
print regressors
contrasts = [["cov", "T", ["group_mean", "z_covariate"], [0, 1]]]
# Subject level contrast source
contrast_source = Node(IdentityInterface(fields=["l1_contrast"]),
iterables=("l1_contrast", exp["contrast_names"]),
name="contrast_source")
# Group workflow
space = args.regspace
wf_name = "_".join([space, args.output])
if space == "mni":
mfx, mfx_input, mfx_output = wf.create_volume_mixedfx_workflow(
wf_name, subject_list, regressors, contrasts, exp)
else:
print 'run mni!'
# Mixed effects inputs
ffxspace = "mni" if space == "mni" else "epi"
ffxsmooth = "unsmoothed" if args.unsmoothed else "smoothed"
mfx_base = op.join("{subject_id}/ffx/%s/%s/{l1_contrast}" %
(ffxspace, ffxsmooth))
templates = dict(copes=op.join(mfx_base, "cope1.nii.gz"))
if space == "mni":
templates.update(
dict(varcopes=op.join(mfx_base, "varcope1.nii.gz"),
dofs=op.join(mfx_base, "tdof_t1.nii.gz")))
else:
templates.update(
dict(reg_file=op.join(anal_dir_base, "{subject_id}/preproc/run_1",
"func2anat_tkreg.dat")))
# Workflow source node
mfx_source = MapNode(
SelectFiles(templates,
base_directory=anal_dir_base,
sort_filelist=True), "subject_id", "mfx_source")
# Workflow input connections
mfx.connect([
(contrast_source, mfx_source, [("l1_contrast", "l1_contrast")]),
(contrast_source, mfx_input, [("l1_contrast", "l1_contrast")]),
(subj_source, mfx_source, [("subject_id", "subject_id")]),
(mfx_source, mfx_input, [("copes", "copes")])
]),
if space == "mni":
mfx.connect([
(mfx_source, mfx_input, [("varcopes", "varcopes"),
("dofs", "dofs")]),
])
else:
mfx.connect([(mfx_source, mfx_input, [("reg_file", "reg_file")]),
(subj_source, mfx_input, [("subject_id", "subject_id")])])
# Mixed effects outputs
mfx_sink = Node(DataSink(base_directory="/".join(
[anal_dir_base, args.output, space]),
substitutions=[("/stats", "/"), ("/_hemi_", "/"),
("_glm_results", "")],
parameterization=True),
name="mfx_sink")
mfx_outwrap = tools.OutputWrapper(mfx, subj_source, mfx_sink, mfx_output)
mfx_outwrap.sink_outputs()
mfx_outwrap.set_mapnode_substitutions(1)
mfx_outwrap.add_regexp_substitutions([(r"_l1_contrast_[-\w]*/", "/"),
(r"_mni_hemi_[lr]h", "")])
mfx.connect(contrast_source, "l1_contrast", mfx_sink, "container")
# Set a few last things
mfx.base_dir = work_dir_base
# Execute
lyman.run_workflow(mfx, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(project["working_dir"])
def __init__(self,
subject_list,
experiment,
roi_name,
orig_type,
force_serial=False,
debug=False):
# Set up basic info
self.subject_list = lyman.determine_subjects(subject_list)
project = lyman.gather_project_info()
self.experiment = experiment
self.roi_name = roi_name
self.orig_type = orig_type
self.debug = debug
if debug:
print "Setting up for %d subjects" % len(subject_list)
print "Experiment name:", experiment
print "ROI name:", roi_name
# Set up directories
if project["default_exp"] is not None and experiment is None:
experiment = project["default_exp"]
self.experiment = experiment
self.data_dir = project["data_dir"]
self.anal_dir = project["analysis_dir"]
# Set up temporary output
self.temp_dir = mkdtemp()
# Set the SUBJECTS_DIR variable for Freesurfer
os.environ["SUBJECTS_DIR"] = self.data_dir
# Set up parallel execution
self.parallel = False
if force_serial:
self.map = map
else:
try:
rc = Client()
self.dv = rc[:]
self.map = self.dv.map_async
# Push SUBJECTS_DIR to engines
self.dv.execute("import os")
self.dv["data_dir"] = self.data_dir
self.dv.execute("os.environ['SUBJECTS_DIR'] = data_dir")
self.parallel = True
except (TimeoutError, IOError):
self.map = map
if debug:
print "Set to run in %s" % ("parallel"
if self.parallel else "serial")
# Set up some persistent templates
self.epi_template = op.join(self.anal_dir, self.experiment, "%(subj)s",
"preproc/run_1/mean_func.nii.gz")
self.fov_template = op.join(self.anal_dir, self.experiment, "%(subj)s",
"preproc/run_1/functional_mask.nii.gz")
self.reg_template = op.join(self.anal_dir, self.experiment, "%(subj)s",
"preproc/run_1/func2anat_tkreg.dat")
self.out_template = op.join(self.data_dir, "%(subj)s",
"masks/%s.nii.gz" % self.roi_name)
if debug:
print "EPI template: %s" % self.epi_template
print "Reg template: %s" % self.reg_template
print "Output template: %s" % self.out_template
# Ensure the output directory will exist
for subj in self.subject_list:
mask_dir = op.join(self.data_dir, subj, "masks")
if not op.exists(mask_dir):
os.mkdir(mask_dir)
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel, args)
if args.experiment is None:
args.experiment = project["default_exp"]
if args.altmodel:
exp_name = "-".join([args.experiment, args.altmodel])
else:
exp_name = args.experiment
# Make sure some paths are set properly
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Set roots of output storage
anal_dir_base = op.join(project["analysis_dir"], exp_name)
work_dir_base = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
# Subject source (no iterables here)
subject_list = lyman.determine_subjects(args.subjects)
subj_source = Node(IdentityInterface(fields=["subject_id"]),
name="subj_source")
subj_source.inputs.subject_id = subject_list
# Set up the regressors and contrasts
regressors = dict(group_mean=[1] * len(subject_list))
contrasts = [["group_mean", "T", ["group_mean"], [1]]]
# Subject level contrast source
contrast_source = Node(IdentityInterface(fields=["l1_contrast"]),
iterables=("l1_contrast", exp["contrast_names"]),
name="contrast_source")
# Group workflow
space = args.regspace
wf_name = "_".join([space, args.output])
if space == "mni":
mfx, mfx_input, mfx_output = wf.create_volume_mixedfx_workflow(
wf_name, subject_list, regressors, contrasts, exp)
else:
mfx, mfx_input, mfx_output = wf.create_surface_ols_workflow(
wf_name, subject_list, exp)
# Mixed effects inputs
ffxspace = "mni" if space == "mni" else "epi"
ffxsmooth = "unsmoothed" if args.unsmoothed else "smoothed"
mfx_base = op.join("{subject_id}/ffx/%s/%s/{l1_contrast}" % (ffxspace,
ffxsmooth))
templates = dict(copes=op.join(mfx_base, "cope1.nii.gz"))
if space == "mni":
templates.update(dict(
varcopes=op.join(mfx_base, "varcope1.nii.gz"),
dofs=op.join(mfx_base, "tdof_t1.nii.gz")))
else:
templates.update(dict(
reg_file=op.join(anal_dir_base,
"{subject_id}/reg/epi/", ffxsmooth,
"run_1/func2anat_tkreg.dat")))
# Workflow source node
mfx_source = MapNode(SelectFiles(templates,
base_directory=anal_dir_base,
sort_filelist=True),
"subject_id",
"mfx_source")
# Workflow input connections
mfx.connect([
(contrast_source, mfx_source,
[("l1_contrast", "l1_contrast")]),
(contrast_source, mfx_input,
[("l1_contrast", "l1_contrast")]),
(subj_source, mfx_source,
[("subject_id", "subject_id")]),
(mfx_source, mfx_input,
[("copes", "copes")])
]),
if space == "mni":
mfx.connect([
(mfx_source, mfx_input,
[("varcopes", "varcopes"),
("dofs", "dofs")]),
])
else:
mfx.connect([
(mfx_source, mfx_input,
[("reg_file", "reg_file")]),
(subj_source, mfx_input,
[("subject_id", "subject_id")])
])
# Mixed effects outputs
mfx_sink = Node(DataSink(base_directory="/".join([anal_dir_base,
args.output,
space]),
substitutions=[("/stats", "/"),
("/_hemi_", "/"),
("_glm_results", "")],
parameterization=True),
name="mfx_sink")
mfx_outwrap = tools.OutputWrapper(mfx, subj_source,
mfx_sink, mfx_output)
mfx_outwrap.sink_outputs()
mfx_outwrap.set_mapnode_substitutions(1)
mfx_outwrap.add_regexp_substitutions([
(r"_l1_contrast_[-\w]*/", "/"),
(r"_mni_hemi_[lr]h", "")
])
mfx.connect(contrast_source, "l1_contrast",
mfx_sink, "container")
# Set a few last things
mfx.base_dir = work_dir_base
# Execute
lyman.run_workflow(mfx, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(project["working_dir"])
import numpy as np
import pandas as pd
from scipy import stats, signal
import statsmodels.api as sm
import nibabel as nib
import seaborn as sns
import matplotlib.pyplot as plt
from surfer import Brain
import moss
from moss import glm
from moss.nipy import VolumeImg
import lyman
subjects = lyman.determine_subjects()
project = lyman.gather_project_info()
data_dir = project["data_dir"]
analysis_dir = project["analysis_dir"]
exp = project["default_exp"]
design_temp = op.join(data_dir, "{}/design/{}.csv")
class SlicePlotter(object):
"""Object to generate single slice images or mosaics of volume results."""
def __init__(self, model, contrast, corrected=True,
stat_thresh=2.3, stat_range=(2, 5),
stat_cmap="OrRd_r", stat_alpha=.85,
sharp=False, label_slices=True):
"""Initialize the object but do not plot anything yet."""
anat_img = nib.load(op.join(data_dir, "average_anat.nii.gz"))
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel, args)
if args.experiment is None:
args.experiment = project["default_exp"]
if args.altmodel:
exp_name = "-".join([args.experiment, args.altmodel])
else:
exp_name = args.experiment
# Make sure some paths are set properly
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Set roots of output storage
anal_dir_base = op.join(project["analysis_dir"], exp_name)
work_dir_base = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
# Subject source (no iterables here)
subject_list = lyman.determine_subjects(args.subjects)
subj_source = Node(IdentityInterface(fields=["subject_id"]),
name="subj_source")
subj_source.inputs.subject_id = subject_list
# Set up the regressors and contrasts
regressors = dict(group_mean=[1] * len(subject_list))
contrasts = [["group_mean", "T", ["group_mean"], [1]]]
# Subject level contrast source
contrast_source = Node(IdentityInterface(fields=["l1_contrast"]),
iterables=("l1_contrast", exp["contrast_names"]),
name="contrast_source")
# Group workflow
space = args.regspace
wf_name = "_".join([space, args.output])
if space == "mni":
mfx, mfx_input, mfx_output = wf.create_volume_mixedfx_workflow(
wf_name, subject_list, regressors, contrasts, exp)
else:
mfx, mfx_input, mfx_output = wf.create_surface_ols_workflow(
wf_name, subject_list, exp)
# Mixed effects inputs
ffxspace = "mni" if space == "mni" else "epi"
ffxsmooth = "unsmoothed" if args.unsmoothed else "smoothed"
mfx_base = op.join("{subject_id}/ffx/%s/%s/{l1_contrast}" %
(ffxspace, ffxsmooth))
templates = dict(copes=op.join(mfx_base, "cope1.nii.gz"))
if space == "mni":
templates.update(
dict(varcopes=op.join(mfx_base, "varcope1.nii.gz"),
dofs=op.join(mfx_base, "tdof_t1.nii.gz")))
else:
templates.update(
dict(reg_file=op.join(anal_dir_base, "{subject_id}/reg/epi/",
ffxsmooth, "run_1/func2anat_tkreg.dat")))
# Workflow source node
mfx_source = MapNode(
SelectFiles(templates,
base_directory=anal_dir_base,
sort_filelist=True), "subject_id", "mfx_source")
# Workflow input connections
mfx.connect([
(contrast_source, mfx_source, [("l1_contrast", "l1_contrast")]),
(contrast_source, mfx_input, [("l1_contrast", "l1_contrast")]),
(subj_source, mfx_source, [("subject_id", "subject_id")]),
(mfx_source, mfx_input, [("copes", "copes")])
]),
if space == "mni":
mfx.connect([
(mfx_source, mfx_input, [("varcopes", "varcopes"),
("dofs", "dofs")]),
])
else:
mfx.connect([(mfx_source, mfx_input, [("reg_file", "reg_file")]),
(subj_source, mfx_input, [("subject_id", "subject_id")])])
# Mixed effects outputs
mfx_sink = Node(DataSink(base_directory="/".join(
[anal_dir_base, args.output, space]),
substitutions=[("/stats", "/"), ("/_hemi_", "/"),
("_glm_results", "")],
parameterization=True),
name="mfx_sink")
mfx_outwrap = tools.OutputWrapper(mfx, subj_source, mfx_sink, mfx_output)
mfx_outwrap.sink_outputs()
mfx_outwrap.set_mapnode_substitutions(1)
mfx_outwrap.add_regexp_substitutions([(r"_l1_contrast_[-\w]*/", "/"),
(r"_mni_hemi_[lr]h", "")])
mfx.connect(contrast_source, "l1_contrast", mfx_sink, "container")
# Set a few last things
mfx.base_dir = work_dir_base
# Execute
lyman.run_workflow(mfx, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(project["working_dir"])
def __init__(self, subject_list, experiment, roi_name, orig_type, force_serial=False, debug=False):
# Set up basic info
self.subject_list = lyman.determine_subjects(subject_list)
project = lyman.gather_project_info()
self.experiment = experiment
self.roi_name = roi_name
self.orig_type = orig_type
self.debug = debug
if debug:
print "Setting up for %d subjects" % len(subject_list)
print "Experiment name:", experiment
print "ROI name:", roi_name
# Set up directories
if project["default_exp"] is not None and experiment is None:
experiment = project["default_exp"]
self.experiment = experiment
self.data_dir = project["data_dir"]
self.anal_dir = project["analysis_dir"]
# Set up temporary output
self.temp_dir = mkdtemp()
# Set the SUBJECTS_DIR variable for Freesurfer
os.environ["SUBJECTS_DIR"] = self.data_dir
# Set up parallel execution
self.parallel = False
if force_serial:
self.map = map
else:
try:
rc = Client()
self.dv = rc[:]
self.map = self.dv.map_async
# Push SUBJECTS_DIR to engines
self.dv.execute("import os")
self.dv["data_dir"] = self.data_dir
self.dv.execute("os.environ['SUBJECTS_DIR'] = data_dir")
self.parallel = True
except (TimeoutError, IOError):
self.map = map
if debug:
print "Set to run in %s" % ("parallel" if self.parallel else "serial")
# Set up some persistent templates
self.epi_template = op.join(self.anal_dir, self.experiment, "%(subj)s", "preproc/run_1/mean_func.nii.gz")
self.fov_template = op.join(self.anal_dir, self.experiment, "%(subj)s", "preproc/run_1/functional_mask.nii.gz")
self.reg_template = op.join(self.anal_dir, self.experiment, "%(subj)s", "preproc/run_1/func2anat_tkreg.dat")
self.out_template = op.join(self.data_dir, "%(subj)s", "masks/%s.nii.gz" % self.roi_name)
if debug:
print "EPI template: %s" % self.epi_template
print "Reg template: %s" % self.reg_template
print "Output template: %s" % self.out_template
# Ensure the output directory will exist
for subj in self.subject_list:
mask_dir = op.join(self.data_dir, subj, "masks")
if not op.exists(mask_dir):
os.mkdir(mask_dir)
def main(arglist):
"""Main function for workflow setup and execution."""
args = parse_args(arglist)
# Get and process specific information
project = lyman.gather_project_info()
exp = lyman.gather_experiment_info(args.experiment, args.altmodel)
if args.experiment is None:
args.experiment = project["default_exp"]
if args.altmodel:
exp_name = "-".join([args.experiment, args.altmodel])
else:
exp_name = args.experiment
# Make sure some paths are set properly
os.environ["SUBJECTS_DIR"] = project["data_dir"]
# Set roots of output storage
anal_dir_base = op.join(project["analysis_dir"], exp_name)
work_dir_base = op.join(project["working_dir"], exp_name)
nipype.config.set("execution", "crashdump_dir", project["crash_dir"])
### Set up group info
## Regular design
group_info = pd.read_csv(group_filepath)
# Subject source (no iterables here)
subject_list = lyman.determine_subjects(args.subjects)
# Additional code (deletion caught by Dan dillon)
subj_source = Node(IdentityInterface(fields=["subject_id"]),
name="subj_source")
subj_source.inputs.subject_id = subject_list
print(group_info)
print(subject_list)
groups = [
group_info[group_info.subid == x].reset_index().at[0, 'group']
for x in subject_list
]
group_vector = [1 if sub == "group1" else 2
for sub in groups] # 1 for group1, 2 for group2
# Set up the regressors and contrasts
regressors = dict(group1_mean=[int(sub == 'group1') for sub in groups],
group2_mean=[int(sub == 'group2') for sub in groups])
print(regressors)
# DECIDE WHICH CONTRAST YOU WANT HERE:
contrasts = [[
contrast_name, "T", ["group1_mean", "group2_mean"], contrast_vals
]]
print('Using this contrast:')
print(contrast_name)
print(contrast_vals)
# Subject level contrast source
contrast_source = Node(IdentityInterface(fields=["l1_contrast"]),
iterables=("l1_contrast", exp["contrast_names"]),
name="contrast_source")
# Group workflow
space = args.regspace
wf_name = "_".join([space, args.output])
if space == "mni":
mfx, mfx_input, mfx_output = wf.create_volume_mixedfx_workflow_groups(
wf_name, subject_list, regressors, contrasts, exp, group_vector)
else:
mfx, mfx_input, mfx_output = wf.create_surface_ols_workflow(
wf_name, subject_list, exp)
# Mixed effects inputs
ffxspace = "mni" if space == "mni" else "epi"
ffxsmooth = "unsmoothed" if args.unsmoothed else "smoothed"
mfx_base = op.join("{subject_id}/ffx/%s/%s/{l1_contrast}" %
(ffxspace, ffxsmooth))
templates = dict(copes=op.join(mfx_base, "cope1.nii.gz"))
if space == "mni":
templates.update(
dict(varcopes=op.join(mfx_base, "varcope1.nii.gz"),
dofs=op.join(mfx_base, "tdof_t1.nii.gz")))
else:
templates.update(
dict(reg_file=op.join(anal_dir_base, "{subject_id}/preproc/run_1",
"func2anat_tkreg.dat")))
# Workflow source node
mfx_source = MapNode(
SelectFiles(templates,
base_directory=anal_dir_base,
sort_filelist=True), "subject_id", "mfx_source")
# Workflow input connections
mfx.connect([
(contrast_source, mfx_source, [("l1_contrast", "l1_contrast")]),
(contrast_source, mfx_input, [("l1_contrast", "l1_contrast")]),
(subj_source, mfx_source, [("subject_id", "subject_id")]),
(mfx_source, mfx_input, [("copes", "copes")])
]),
if space == "mni":
mfx.connect([
(mfx_source, mfx_input, [("varcopes", "varcopes"),
("dofs", "dofs")]),
])
else:
mfx.connect([(mfx_source, mfx_input, [("reg_file", "reg_file")]),
(subj_source, mfx_input, [("subject_id", "subject_id")])])
# Mixed effects outputs
mfx_sink = Node(DataSink(base_directory="/".join(
[anal_dir_base, args.output, space]),
substitutions=[("/stats", "/"), ("/_hemi_", "/"),
("_glm_results", "")],
parameterization=True),
name="mfx_sink")
mfx_outwrap = tools.OutputWrapper(mfx, subj_source, mfx_sink, mfx_output)
mfx_outwrap.sink_outputs()
mfx_outwrap.set_mapnode_substitutions(1)
mfx_outwrap.add_regexp_substitutions([(r"_l1_contrast_[-\w]*/", "/"),
(r"_mni_hemi_[lr]h", "")])
mfx.connect(contrast_source, "l1_contrast", mfx_sink, "container")
# Set a few last things
mfx.base_dir = work_dir_base
# Execute
lyman.run_workflow(mfx, args=args)
# Clean up
if project["rm_working_dir"]:
shutil.rmtree(project["working_dir"])
redirect, send_file)
import lyman
project = lyman.gather_project_info()
default_exp = project["default_exp"]
parser = argparse.ArgumentParser()
parser.add_argument("-subjects", nargs="*")
parser.add_argument("-experiment", default=default_exp)
parser.add_argument("-port", type=int, default=5000)
parser.add_argument("-external", action="store_true")
parser.add_argument("-debug", action="store_true")
args = parser.parse_args(sys.argv[1:])
subjects = lyman.determine_subjects(args.subjects)
exp_base = args.experiment
app = Flask(__name__)
def basic_info(experiment=exp_base):
"""Basic information needed before any report options are set."""
experiments = list_experiments()
exp = experiment_info(experiment)
subjects_size = min(len(subjects), 10)
runs = range(1, exp["n_runs"] + 1)
contrasts = exp["contrast_names"]
