def Check(self,
SettingFileName,
isOne=False,
SubID=None,
RunID=None,
ConID=None):
import numpy as np
import os
from Base.utility import fixstr, setParameters3, strRange, strMultiRange
from Base.Setting import Setting
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False
else:
if isOne:
Subjects = [SubID]
Counters = [[ConID]]
Runs = [[RunID]]
else:
Subjects = strRange(setting.SubRange, Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange, SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False
Runs = strMultiRange(setting.RunRange, SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Checking script for Subject %d ..." % (s))
for r in Runs[si]:
ScriptAddr = setParameters3(setting.Script, setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
if os.path.isfile(ScriptAddr):
print("CHECK: " + ScriptAddr + " - checked!")
else:
print("CHECK: " + ScriptAddr + " - not found!")
return False
return True
def run(self,SettingFileName, betcmd=None):
import os
from Base.utility import fixstr,setParameters3, strRange, strMultiRange
from Base.Setting import Setting
if betcmd is None:
print("Cannot find bet cmd")
return
if not os.path.isfile(betcmd):
print("Cannot find bet cmd")
return
setting = Setting()
setting.Load(SettingFileName)
if (setting.empty) or (setting.Anat == False) :
if setting.empty:
print("Error in loading the setting file!")
if not setting.Anat:
print("This feature is disable for in setting file. Please turn it on from Advance menu!")
return False
else:
Subjects = strRange(setting.SubRange,Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange,SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False
Runs = strMultiRange(setting.RunRange,SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False
Jobs = list()
for sindx, s in enumerate(Subjects):
for cnt in Counters[sindx]:
print("Analyzing Subject %d, Counter %d ..." % (s, cnt))
InAddr = setParameters3(setting.AnatDIR,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
InFile = setParameters3(setting.AnatDIR,"", fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
OutAddr = setParameters3(setting.BET,setting.mainDIR,fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
PDFAddr = setParameters3(setting.BETPDF,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
if not os.path.isfile(InAddr):
print(InAddr, " - file not find!")
return False
else:
files = [OutAddr, PDFAddr]
thread = BrainExtractorThread(bet=betcmd, InAddr=InAddr, OutAddr=OutAddr, PDFAddr=PDFAddr,\
InFile=InFile, files=files)
Jobs.append(["BrainExtractor", InFile, thread])
print("Job: Anatomical Brain Extractor for Subject %d, Counter %d is created." % (s, cnt))
return True, Jobs
def run(self,SettingFileName):
from Base.utility import fixstr,setParameters3, strRange, strMultiRange
from Base.Setting import Setting
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False
else:
Subjects = strRange(setting.SubRange,Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange,SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False
Runs = strMultiRange(setting.RunRange,SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Analyzing Subject %d, Counter %d ..." % (s, cnt))
for r in Runs[si]:
ScriptAddr = setParameters3(setting.Script,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
ScriptOutputAddr = setParameters3(setting.Analysis,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
BOLDaddr = setParameters3(setting.BOLD,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
MRIFile = nb.load(BOLDaddr)
# Generate Script
scriptFile = open(ScriptAddr,"w")
scriptFile.write("\n# FEAT version number\nset fmri(version) 6.00\n\n# Are we in MELODIC?\nset fmri(inmelodic) 0\n\n")
scriptFile.write("# Analysis level\n# 1 : First-level analysis\n# 2 : Higher-level analysis\nset fmri(level) 1\n\n")
scriptFile.write("# Which stages to run\n# 0 : No first-level analysis (registration and/or group stats only)\n")
scriptFile.write("# 7 : Full first-level analysis\n# 1 : Pre-processing\n# 2 : Statistics\nset fmri(analysis) 7\n\n")
scriptFile.write("# Use relative filenames\nset fmri(relative_yn) 0\n\n")
scriptFile.write("# Balloon help\nset fmri(help_yn) 1\n\n")
scriptFile.write("# Run Featwatcher\nset fmri(featwatcher_yn) 0\n\n")
scriptFile.write("# Cleanup first-level standard-space images\nset fmri(sscleanup_yn) 0\n\n")
scriptFile.write("# Output directory\nset fmri(outputdir) \"" + ScriptOutputAddr + "\"\n\n")
# TR
scriptFile.write("# TR(s)\nset fmri(tr) %0.6f \n\n" % setting.TR)
# Total Volumes
if setting.TotalVol == 0:
print("Auto Detect Total Volumes = " + str(get_mri_shape(MRIFile)[3]) + ", File: " + BOLDaddr)
scriptFile.write("# Total volumes\nset fmri(npts) " + str(get_mri_shape(MRIFile)[3]) + "\n\n")
else:
scriptFile.write("# Total volumes\nset fmri(npts) " + str(setting.TotalVol) + "\n\n")
# Delete Volumes
scriptFile.write("# Delete volumes\nset fmri(ndelete) " + str(setting.DeleteVol) + "\n\n")
scriptFile.write("# Perfusion tag/control order\nset fmri(tagfirst) 1\n\n")
scriptFile.write("# Number of first-level analyses\nset fmri(multiple) 1\n\n")
scriptFile.write("# Higher-level input type\n# 1 : Inputs are lower-level FEAT directories\n# 2 : Inputs are cope images from FEAT directories\nset fmri(inputtype) 2\n\n")
scriptFile.write("# Carry out pre-stats processing?\nset fmri(filtering_yn) 1\n\n")
scriptFile.write("# Brain/background threshold, %\nset fmri(brain_thresfh) 10\n\n")
scriptFile.write("# Critical z for design efficiency calculation\nset fmri(critical_z) " + str(setting.DEZT) + "\n\n")
scriptFile.write("# Noise level\nset fmri(noise) " + str(setting.DENL) + "\n\n# Noise AR(1)\nset fmri(noisear) " + str(setting.DETS) + "\n\n")
# Motion Correction: ALWAYS ON
scriptFile.write("# Motion correction\n# 0 : None\n# 1 : MCFLIRT\nset fmri(mc) 1\n\n")
scriptFile.write("# Spin-history (currently obsolete)\nset fmri(sh_yn) 0\n\n")
scriptFile.write("# B0 fieldmap unwarping?\nset fmri(regunwarp_yn) 0\n\n")
scriptFile.write("# EPI dwell time (ms)\nset fmri(dwell) 0.7\n\n")
scriptFile.write("# EPI TE (ms)\nset fmri(te) 35\n\n")
scriptFile.write("# % Signal loss threshold\nset fmri(signallossthresh) 10\n\n")
scriptFile.write("# Unwarp direction\nset fmri(unwarp_dir) y-\n\n")
scriptFile.write("# Slice timing correction\n# 0 : None\n# 1 : Regular up (0, 1, 2, 3, ...)\n# 2 : Regular down\n")
scriptFile.write("# 3 : Use slice order file\n# 4 : Use slice timings file\n# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )\n")
# Slice Timing
scriptFile.write("set fmri(st) " + str(setting.TimeSlice) + "\n\n")
scriptFile.write("# Slice timings file\nset fmri(st_file) \"\"\n\n")
scriptFile.write("# BET brain extraction\nset fmri(bet_yn) 1\n\n")
# FWHM
scriptFile.write("# Spatial smoothing FWHM (mm)\nset fmri(smooth) " + str(setting.FWHM) + "\n\n")
scriptFile.write("# Intensity normalization\nset fmri(norm_yn) 0\n\n")
scriptFile.write("# Perfusion subtraction\nset fmri(perfsub_yn) 0\n\n")
scriptFile.write("# Highpass temporal filtering\nset fmri(temphp_yn) 1\n\n")
scriptFile.write("# Lowpass temporal filtering\nset fmri(templp_yn) 0\n\n")
scriptFile.write("# MELODIC ICA data exploration\nset fmri(melodic_yn) 0\n\n")
scriptFile.write("# Carry out main stats?\nset fmri(stats_yn) 1\n\n")
scriptFile.write("# Carry out prewhitening?\nset fmri(prewhiten_yn) 1\n\n")
scriptFile.write("# Add motion parameters to model\n# 0 : No\n# 1 : Yes\nset fmri(motionevs) 1\nset fmri(motionevsbeta) \"\"\nset fmri(scriptevsbeta) \"\"\n\n")
scriptFile.write("# Robust outlier detection in FLAME?\nset fmri(robust_yn) 0\n\n")
scriptFile.write("# Higher-level modelling\n# 3 : Fixed effects\n# 0 : Mixed Effects: Simple OLS\n# 2 : Mixed Effects: FLAME 1\n# 1 : Mixed Effects: FLAME 1+2\nset fmri(mixed_yn) 2\n\n")
# Conditions
ConditionFile = setParameters3(setting.EventFolder,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, fixstr(cnt, setting.ConLen, setting.ConPer)) + setting.CondPre + ".mat"
Cond = io.loadmat(ConditionFile)
Conditions = Cond["Cond"]
CondLen = len(Conditions)
scriptFile.write("# Number of EVs\nset fmri(evs_orig) "+str(CondLen)+"\nset fmri(evs_real) "+str(CondLen)+"\nset fmri(evs_vox) 0\n\n")
scriptFile.write("# Number of contrasts\nset fmri(ncon_orig) "+str(CondLen)+"\nset fmri(ncon_real) "+str(CondLen)+"\n\n")
scriptFile.write("# Number of F-tests\nset fmri(nftests_orig) 0\nset fmri(nftests_real) 0\n\n")
scriptFile.write("# Add constant column to design matrix? (obsolete)\nset fmri(constcol) 0\n\n")
scriptFile.write("# Carry out post-stats steps?\nset fmri(poststats_yn) 1\n\n")
scriptFile.write("# Pre-threshold masking?\nset fmri(threshmask) \"\"\n\n")
# Clustering
scriptFile.write("# Thresholding\n# 0 : None\n# 1 : Uncorrected\n# 2 : Voxel\n# 3 : Cluster\nset fmri(thresh) 3\n\n")
scriptFile.write("# P threshold\nset fmri(prob_thresh) " + str(setting.CTPT) + "\n\n")
scriptFile.write("# Z threshold\nset fmri(z_thresh) " + str(setting.CTZT) + "\n\n")
scriptFile.write("# Z min/max for colour rendering\n# 0 : Use actual Z min/max\n# 1 : Use preset Z min/max\nset fmri(zdisplay) 0\n\n")
scriptFile.write("# Z min in colour rendering\nset fmri(zmin) 2\n\n")
scriptFile.write("# Z max in colour rendering\nset fmri(zmax) 8\n\n")
scriptFile.write("# Colour rendering type\n# 0 : Solid blobs\n# 1 : Transparent blobs\nset fmri(rendertype) 1\n\n")
scriptFile.write("# Background image for higher-level stats overlays\n# 1 : Mean highres\n# 2 : First highres\n# 3 : Mean functional\n# 4 : First functional\n# 5 : Standard space template\nset fmri(bgimage) 1\n\n")
scriptFile.write("# Create time series plots\nset fmri(tsplot_yn) 1\n\n")
scriptFile.write("# Registration to initial structural\nset fmri(reginitial_highres_yn) 0\n\n")
scriptFile.write("# Search space for registration to initial structural\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(reginitial_highres_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to initial structural\nset fmri(reginitial_highres_dof) 3\n\n")
# Anat
if setting.Anat:
scriptFile.write("# Registration to main structural\nset fmri(reghighres_yn) 1\n\n")
scriptFile.write("# Search space for registration to main structural\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(reghighres_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to main structural\nset fmri(reghighres_dof) 12\n\n")
else:
scriptFile.write("# Registration to main structural\nset fmri(reghighres_yn) 0\n\n")
scriptFile.write("# Search space for registration to main structural\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(reghighres_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to main structural\nset fmri(reghighres_dof) BBR\n\n")
# Standard Space
scriptFile.write("# Registration to standard image?\nset fmri(regstandard_yn) 1\n\n")
scriptFile.write("# Use alternate reference images?\nset fmri(alternateReference_yn) 0\n\n")
# Get {FSLDIR}
#StandardTemp = os.path.dirname(os.path.realpath(__file__)) + "/MNI152_T1_2mm_brain"
scriptFile.write("# Standard image\nset fmri(regstandard) \"" + setting.MNISpace + "\"\n\n")
scriptFile.write("# Search space for registration to standard space\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(regstandard_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to standard space\nset fmri(regstandard_dof) 12\n\n")
scriptFile.write("# Do nonlinear registration from structural to standard space?\nset fmri(regstandard_nonlinear_yn) 0\n\n")
scriptFile.write("# Control nonlinear warp field resolution\nset fmri(regstandard_nonlinear_warpres) 10 \n\n")
# High Pass
scriptFile.write("# High pass filter cutoff\nset fmri(paradigm_hp) %d\n\n" % setting.HighPass)
# Total Voxel
TotalVoxel = get_mri_shape(MRIFile)[0] * get_mri_shape(MRIFile)[1] * get_mri_shape(MRIFile)[2] * get_mri_shape(MRIFile)[3]
scriptFile.write("# Total voxels\nset fmri(totalVoxels) " + str(TotalVoxel) + "\n\n\n")
scriptFile.write("# Number of lower-level copes feeding into higher-level analysis\nset fmri(ncopeinputs) 0\n\n")
scriptFile.write("# 4D AVW data or FEAT directory (1)\nset feat_files(1) \"" + BOLDaddr + "\"\n\n")
scriptFile.write("# Add confound EVs text file\nset fmri(confoundevs) 0\n\n")
# Align to structural MRI
if setting.Anat:
AnatAddr = setParameters3(setting.BET,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),"",setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
scriptFile.write("# Subject's structural image for analysis 1\nset highres_files(1) \"" + AnatAddr + "\"\n\n")
# Condition Files
for cond in range(1,CondLen + 1):
scriptFile.write("# EV " + str(cond) + " title\nset fmri(evtitle"+str(cond)+") \""+Conditions[cond-1][1][0]+"\"\n\n")
scriptFile.write("# Basic waveform shape (EV " + str(cond) + ")\n# 0 : Square\n# 1 : Sinusoid\n# 2 : Custom (1 entry per volume)\n# 3 : Custom (3 column format)\n# 4 : Interaction\n# 10 : Empty (all zeros)\nset fmri(shape" + str(cond) + ") 3\n\n")
scriptFile.write("# Convolution (EV " + str(cond) + ")\n# 0 : None\n# 1 : Gaussian\n# 2 : Gamma\n# 3 : Double-Gamma HRF\n# 4 : Gamma basis functions\n# 5 : Sine basis functions\n# 6 : FIR basis functions\nset fmri(convolve" + str(cond) + ") 2\n\n")
scriptFile.write("# Convolve phase (EV " + str(cond) + ")\nset fmri(convolve_phase" + str(cond) + ") 0\n\n")
scriptFile.write("# Apply temporal filtering (EV " + str(cond) + ")\nset fmri(tempfilt_yn" + str(cond) + ") 1\n\n")
scriptFile.write("# Add temporal derivative (EV " + str(cond) + ")\nset fmri(deriv_yn" + str(cond) + ") 0\n\n")
ConditionFile = setParameters3(setting.EventFolder,setting.mainDIR, fixstr(s, setting.SubLen,setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer)) + setting.CondPre + "_" + str(cond) + ".tab"
scriptFile.write("# Custom EV file (EV " + str(cond) + ")\nset fmri(custom" + str(cond) + ") \"" + ConditionFile + "\"\n\n")
scriptFile.write("# Gamma sigma (EV " + str(cond) + ")\nset fmri(gammasigma" + str(cond) + ") 3\n\n")
scriptFile.write("# Gamma delay (EV " + str(cond) + ")\nset fmri(gammadelay" + str(cond) + ") 6\n\n")
for ev in range(0,CondLen + 1):
scriptFile.write("# Orthogonalise EV " + str(cond) + " wrt EV " + str(ev) + "\nset fmri(ortho" + str(cond) + "." + str(ev) + ") 0\n\n")
scriptFile.write("# Contrast & F-tests mode\n# real : control real EVs\n# orig : control original EVs\nset fmri(con_mode_old) orig\nset fmri(con_mode) orig\n\n")
# Contrast & F-tests mode
for cond in range(1,CondLen + 1):
scriptFile.write("# Display images for contrast_real " + str(cond) + "\nset fmri(conpic_real." + str(cond) + ") 1\n\n")
scriptFile.write("# Title for contrast_real " + str(cond) + "\nset fmri(conname_real." + str(cond) + ") \"" + Conditions[cond-1][1][0] + "\"\n\n")
for ev in range(1, CondLen + 1):
if ev == cond:
scriptFile.write("# Real contrast_real vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_real" + str(cond) + "." + str(ev) + ") " + str(CondLen) + "\n\n")
else:
scriptFile.write("# Real contrast_real vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_real" + str(cond) + "." + str(ev) + ") -1\n\n")
for cond in range(1,CondLen + 1):
scriptFile.write("# Display images for contrast_orig " + str(cond) + "\nset fmri(conpic_orig." + str(cond) + ") 1\n\n")
scriptFile.write("# Title for contrast_orig " + str(cond) + "\nset fmri(conname_orig." + str(cond) + ") \"" + Conditions[cond-1][1][0] + "\"\n\n")
for ev in range(1, CondLen + 1):
if ev == cond:
scriptFile.write("# Real contrast_orig vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_orig" + str(cond) + "." + str(ev) + ") " + str(CondLen) + "\n\n")
else:
scriptFile.write("# Real contrast_orig vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_orig" + str(cond) + "." + str(ev) + ") -1\n\n")
scriptFile.write("# Contrast masking - use >0 instead of thresholding?\nset fmri(conmask_zerothresh_yn) 0\n\n")
scriptFile.write("")
for cond in range(1,CondLen + 1):
for ev in range(1,CondLen + 1):
if cond != ev:
scriptFile.write("# Mask real contrast/F-test " + str(cond) + " with real contrast/F-test " + str(ev) + "?\nset fmri(conmask" + str(cond) + "_" + str(ev) + ") 0\n\n")
scriptFile.write("# Do contrast masking at all?\nset fmri(conmask1_1) 0\n\n")
scriptFile.write("##########################################################\n# Now options that don't appear in the GUI\n\n")
scriptFile.write("# Alternative (to BETting) mask image\nset fmri(alternative_mask) \"\"\n\n")
scriptFile.write("# Initial structural space registration initialisation transform\nset fmri(init_initial_highres) \"\"\n\n")
scriptFile.write("# Structural space registration initialisation transform\nset fmri(init_highres) \"\"\n\n")
scriptFile.write("# Standard space registration initialisation transform\nset fmri(init_standard) \"\"\n\n")
scriptFile.write("# For full FEAT analysis: overwrite existing .feat output dir?\nset fmri(overwrite_yn) 0")
scriptFile.close()
print("SCRIPT: " + ScriptAddr + " is generated!")
def Run(self,
SettingFileName,
isOne=False,
Remove=True,
feat=None,
SubID=None,
RunID=None,
ConID=None):
import numpy as np
import os, subprocess
from Base.utility import fixstr, setParameters3, strRange, strMultiRange
from Base.Setting import Setting
if (feat == None) or (os.path.isfile(feat) == False):
print("Cannot find feat cmd!")
return False, None
Jobs = list()
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False, None
else:
if isOne:
Subjects = [SubID]
Counters = [[ConID]]
Runs = [[RunID]]
else:
Subjects = strRange(setting.SubRange, Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False, None
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange, SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False, None
Runs = strMultiRange(setting.RunRange, SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False, None
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Run script for Subject %d ..." % (s))
for r in Runs[si]:
ScriptAddr = setParameters3(setting.Script,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
ScriptTitle = setParameters3(setting.Script, "", fixstr(s, setting.SubLen, setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
ScriptOutputAddr = setParameters3(setting.Analysis, setting.mainDIR,
fixstr(s, setting.SubLen, setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer)) + ".feat"
files = [ScriptOutputAddr + "/filtered_func_data.nii.gz", ScriptOutputAddr + \
"/mask.nii.gz", ScriptOutputAddr + "/cluster_mask_zstat1.nii.gz"]
cmd = ScriptAddr
report = ScriptOutputAddr + "/report_log.html"
thread = PreprocessThread(feat=feat, cmd=cmd, report=report, files=files, \
remove=Remove, removefile=ScriptOutputAddr)
Jobs.append(["Preprocess", ScriptTitle, thread])
print("Job for " + ScriptAddr + " - is created!")
return True, Jobs
def run(self, SettingFileName):
import numpy as np
import scipy.io as io
import os
from Base.utility import fixstr, setParameters3
from Base.Setting import Setting, strRange, strMultiRange
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False
else:
self.ConditionTitles = []
Events = []
Subjects = strRange(setting.SubRange, Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange, SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False
Runs = strMultiRange(setting.RunRange, SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False
# COLECT ALL EVENTS AND CALCULATE THE LIST OF CONDITION
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Analyzing Subject %d, Counter %d ..." % (s, cnt))
for r in Runs[si]:
# Event File Check
EventAddr = setParameters3(setting.Onset,setting.mainDIR,fixstr(s, setting.SubLen, setting.SubPer)\
,fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
EventFolder = setParameters3(setting.EventFolder,setting.mainDIR,fixstr(s, setting.SubLen, setting.SubPer)\
,fixstr(r, setting.RunLen, setting.RunPer), setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
#EventFolder = SubDIR + "/func/" + "sub-" + fixstr(s, SubLen, setting.SubPer) + "_task-" + setting.Task + "_run-" + \
#fixstr(r, RunLen, setting.RunPer) + "_events/"
MatAddr = EventFolder + setting.CondPre + ".mat"
if not os.path.isfile(EventAddr):
print(EventAddr, " - file not find!")
return False
else:
file = open(EventAddr, "r")
lines = file.readlines()
file.close()
dir = {}
dir.clear()
for k in range(0, len(lines)):
Event = lines[k].rsplit()
try:
allvars = dict(locals(), **globals())
exec(setting.EventCodes, allvars, allvars)
except Exception as e:
print(
"Event codes generated following error:\n"
)
print(e)
return False
try:
RowStartID = allvars['RowStartID']
except:
print(
"Cannot find RowStartID variable in event code"
)
return False
try:
Condition = allvars['Condition']
except:
print(
"Cannot find Condition variable in event code"
)
return False
try:
Onset = allvars['Onset']
except:
print(
"Cannot find Onset variable in event code"
)
return False
try:
Duration = allvars['Duration']
except:
print(
"Cannot find Duration variable in event code"
)
return False
try:
Skip = int(allvars["Skip"])
except:
print(
"Cannot find Skip variable in event code"
)
return False
if RowStartID <= k and Skip == 0:
# Create Condition Directory
try:
value = dir[Condition]
value.append(
[float(Onset),
float(Duration)])
dir[Condition] = value
except KeyError:
value = list()
value.append(
[float(Onset),
float(Duration)])
dir[Condition] = value
for condinx, cond in enumerate(dir):
self.add_condTitle(
title=cond,
ConditionTitles=self.ConditionTitles)
Events.append([MatAddr, EventFolder, dir])
print(
"Subject %d, Counter %d, Run %d is verified." %
(s, cnt, r))
# Create Standard Condition Titles list
conditions = []
for cond in self.ConditionTitles:
conditions.append([
setting.CondPre + "_" +
str(self.get_condID(cond[0], self.ConditionTitles)),
cond[0]
])
conditions = np.array(conditions, dtype=object)
# Normalized the condition titile for all events
StandardEvents = []
for event in Events:
StandardEvent = dict()
StandardEvent["Cond"] = conditions
for cond in event[2]:
StandardEvent[setting.CondPre + "_" + str(
self.get_condID(
cond, self.ConditionTitles))] = event[2][cond]
# Add list of titles
StandardEvents.append([event[0], event[1], StandardEvent])
print("Events were normalized! Generating event files ...")
# Save Files
for event in StandardEvents:
try:
os.mkdir(event[1])
except:
pass
io.savemat(event[0], event[2])
for tabs in event[2]:
if tabs == "Cond":
conFile = open(event[1] + tabs + ".txt", "w")
for con in event[2][tabs]:
conFile.write(
str(con[0]) + "\t" + str(con[1]) + "\n")
conFile.close()
else:
tabFile = open(event[1] + tabs + ".tab", "w")
for onset in event[2][tabs]:
tabFile.write(
str(onset[0]) + "\t" + str(onset[1]) + "\t1\n")
tabFile.close()
print("EVENT: " + event[1] + " is generated!")
# Check Tab File
for cond in conditions:
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print(
"Checking Tab Files: Subject %d, Counter %d ..." %
(s, cnt))
for r in Runs[si]:
EventFolder = setParameters3(setting.EventFolder, setting.mainDIR,
fixstr(s, setting.SubLen, setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
fname = EventFolder + cond[0] + '.tab'
if os.path.isfile(fname):
print(fname + " - is okay.")
else:
tabfile = open(fname, "w")
tabfile.write("0\t0\t0\n")
tabfile.close()
print(fname + " - is EMPTY!")
# Report
print("List of generated conditions:")
print("Condition ID\tCondition Title")
for cond in conditions:
print("\t" + cond[0] + "\t\t\t" + cond[1])