def gen_parc_masks(rois, roiNums, parcVol, outDir,
doVolStats=True, redo=False, logFN=None):
import os
import numpy as np
from scipy.io import savemat as savemat
from scai_utils import check_bin_path, check_file, \
cmd_stdout, saydo, info_log, error_log
check_bin_path("fslstats", logFN=logFN)
volStats = {"roiName": [], "nVoxels": [], "mm3": []}
for (i0, roi) in enumerate(rois):
roiNum = roiNums[i0]
maskFN = os.path.join(outDir, "%s.diff.nii.gz" % roi)
binCmd = "mri_binarize --i %s --match %d --o %s" % \
(parcVol, roiNum, maskFN)
if not os.path.isfile(maskFN) or redo:
saydo(binCmd, logFN=logFN)
check_file(maskFN, logFN=logFN)
#= Volume stats =#
(so, se) = cmd_stdout("fslstats %s -V" % maskFN)
assert(len(se) == 0)
so = so.split(" ")
assert(len(so) >= 2)
volStats["nVoxels"].append(int(so[0]))
volStats["mm3"].append(float(so[1]))
volStats["roiName"].append(roi)
if doVolStats:
volStats["roiName"] = np.array(volStats["roiName"])
volStats["nVoxels"] = np.array(volStats["nVoxels"])
volStats["mm3"] = np.array(volStats["mm3"])
volStatsFN = os.path.join(outDir, "vol_stats.mat")
savemat(volStatsFN, volStats)
check_file(volStatsFN, logFN=logFN)
info_log("INFO: %s: Saved volume stats of the mask files at\n\t%s" \
% (gen_parc_masks.__name__, volStatsFN), logFN=logFN)
def generate_design_matrix(isAWS, matFN, bReverse=False):
# Input arguments:
# isAWS: vector of 0's and 1's
# matFN: output design matrix .mat file name
# bReverse: if AWS should be set to -1 and ANS to +1 (default: no)
if len(isAWS) < 2:
error_log("The design matrix cannot be generated because there are fewer than two subjects")
if not matFN.endswith(".mat"):
error_log("The input .mat file name %s has a wrong extension name" % matFN)
X_line = 'X = ['
for (i0, t_isAWS) in enumerate(isAWS):
t_x = (float(t_isAWS) * 2.0 - 1.0)
if bReverse:
X_line += "%.1f; " % -t_x
else:
X_line += "%.1f; " % t_x
X_line = X_line[:-2] + "];\n"
X_line += "X = [ones(%d , 1), X];\n" % len(isAWS)
X_line += "save('%s', 'X', '-v4');\n" % os.path.abspath(matFN)
print(X_line) # DEBUG
(t_path, t_fn) = os.path.split(os.path.abspath(matFN))
mScriptGenX = os.path.join(t_path, 'gen_%s' % t_fn.replace(".mat", ".m"))
mScriptGenX_f = open(mScriptGenX, "wt")
mScriptGenX_f.write(X_line)
mScriptGenX_f.close()
check_file(mScriptGenX)
matlabCmd = "%s -nosplash -nodesktop -r 'run %s; exit; '" % \
(MATLAB_BIN, mScriptGenX)
saydo(matlabCmd)
check_file(matFN)
def get_parc_stats(fsDir, subjID, parcName, bVerbose=False):
import sys, os
import tempfile
from scai_utils import (
check_dir,
check_file,
check_bin_path,
info_log,
cmd_stdout,
saydo,
read_text_file,
remove_empty_strings,
)
# === Constants ===#
hemis = ["lh", "rh"]
segStatsBin = "mri_segstats"
# === Implementation ===#
check_bin_path(segStatsBin)
sDir = os.path.join(fsDir, subjID)
check_dir(sDir)
lblDir = os.path.join(sDir, "label")
check_dir(sDir)
if bVerbose:
info_log("Label directory = %s" % lblDir)
morphInfo = {}
rois = []
area_mm2 = []
for (i0, hemi) in enumerate(hemis):
if bVerbose:
info_log("Working on hemisphere: %s" % hemi)
annot = os.path.join(lblDir, "%s.%s.annot" % (hemi, parcName))
check_file(annot)
tmpSum = tempfile.mktemp()
cmd = "%s --annot %s %s %s --sum %s" % (segStatsBin, subjID, hemi, parcName, tmpSum)
saydo(cmd)
check_file(tmpSum)
if bVerbose:
print("Intermediate results saved at: %s" % tmpSum)
t = read_text_file(tmpSum)
for (i0, tline) in enumerate(t):
tline = tline.strip()
if len(tline) == 0:
continue
elif tline.startswith("#"):
continue
t_items = remove_empty_strings(tline.split())
if len(t_items) != 5:
continue
t_roi = t_items[4]
if t_roi.lower() == "none":
continue
rois.append("%s_%s" % (hemi, t_roi))
area_mm2.append(float(t_items[3]))
saydo("rm -rf %s" % tmpSum)
morphInfo["rois"] = rois
morphInfo["area_mm2"] = area_mm2
return morphInfo
"nii", "func2struct.bbr.mat")
check_file(bbrMat)
cvConFN = os.path.join(L1Dir, "con_%.4d.commVol.nii.gz" % \
args.contrastNum)
#=== Locate the warp files ===#
fnirtWarp = os.path.join(args.batchBase, sID,
"fnirt",
"fnirt_to_%s_warp.nii.gz" % templateSuffix)
check_file(fnirtWarp)
if args.bRedo or not os.path.isfile(cvConFN):
warpCmd = "applywarp --ref=%s --in=%s --warp=%s --premat=%s --out=%s" % \
(VOL_TEMPLATE, conFN, fnirtWarp, bbrMat, cvConFN) \
+ " --interp=trilinear"
saydo(warpCmd)
check_file(cvConFN)
cvConFNs.append(cvConFN)
else:
#== Use vol2surf command to project the contrast values to the subject's own surface ===#
#== Then use mris_preproc to project the data from the subject's own surface to the common space (fsaverage) ==#
for hemi in HEMIS:
surfConFN = os.path.join(L1Dir, "con_%.4d.%s.mgz" % \
(args.contrastNum, hemi))
if args.bRedo or not os.path.isfile(surfConFN):
projCmd = "mri_vol2surf --mov %s --reg %s --o %s --hemi %s --trgsubject %s --noreshape --interp trilin" % \
(conFN, bbrDat, surfConFN, hemi, sID)
saydo(projCmd)
check_file(surfConFN)
parser.add_argument("trg_sID", type=str, help="Target subject ID")
parser.add_argument("trg_dir", type=str, help="Destination path for writing the new label files");
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
args = parser.parse_args()
src_sID = args.src_sID
src_dir = args.src_dir
hemi = args.hemi
trg_sID = args.trg_sID
trg_dir = args.trg_dir
if not os.path.isdir(trg_dir):
saydo("mkdir %s"%trg_dir)
# Determine the set of ROIs
cwd0 = os.getcwd()
srcdir = os.path.join(FSDATA_DIR, src_sID, "label", src_dir)
if not os.path.isdir(srcdir):
raise Exception, "Cannot find source directory at location: %s"%(srcdir)
d0 = glob.glob(os.path.join(srcdir, "%s.*.label"%(hemi)))
if len(d0) == 0:
raise Exception, "Found no files in source directory: %s"%(srcdir)
d0.sort()
rois = []
for fn in d0:
[fpath, fnn] = os.path.split(fn)
check_dir(fsDataDir)
boldDir = os.path.join(sDataDir, "bold")
check_dir(boldDir)
#=== Look for the fmri_model.mat and fmri_contrasts.mat files ===#
modelMat = os.path.join(sDataDir, "fmri_model.mat")
check_file(modelMat)
info_log("modelMat = %s" % modelMat)
contrMat = os.path.join(sDataDir, "fmri_contrasts.mat")
check_file(contrMat)
info_log("contrMat = %s" % contrMat)
#=== Copy over the .mat files ===#
saydo("cp %s %s/" % (modelMat, sBatchDataDir))
saydo("cp %s %s/" % (contrMat, sBatchDataDir))
#=== Load model mat and determine how many runs were collected ===#
from scipy.io import loadmat
mdl = loadmat(modelMat)
nRuns = len(mdl["sess"][0])
info_log("model file %s contains %d runs." % (modelMat, nRuns))
#=== Look for raw bold volumes ===#
info_log("Raw BOLD image dir = %s" % boldDir)
boldWC = machineSettings[hostName]["boldVolWC"].replace("{subjID}", sID)
boldWC = os.path.join(boldDir, boldWC)
def run_probtrackx(seedMask,
targMask,
bedpBase,
brainMask,
outDir,
doSeedNorm=True,
doSize=True,
doTargMaskedFDT=True,
ccStop=False,
bRedo=False,
logFN=None):
#=========================================================#
# Mode 1: from seed to targ
# Specify both seedMask and targMask
#
# Mode 2: from seed to all
# Specify only seedMask; set targMask=None
#
# Options:
# ccStop: Use corpus callosum stop mask
#
#=========================================================#
import os
from scai_utils import check_file, check_dir, check_bin_path, \
saydo, cmd_stdout, info_log, error_log
from mri_utils import nz_voxels
#== Get seed and targ nvox ==#
check_file(seedMask, logFN=logFN)
(seed_nVoxels, seed_mm3) = nz_voxels(seedMask)
seed_nVoxels = float(seed_nVoxels)
#assert(seed_nVoxels > 0)
if targMask != None:
check_file(targMask, logFN=logFN)
(targ_nVoxels, targ_mm3) = nz_voxels(targMask)
targ_nVoxels = float(targ_nVoxels)
assert (targ_nVoxels > 0)
check_bin_path("probtrackx", logFN=logFN)
check_dir(outDir, logFN=logFN)
if targMask != None:
#= Prepare waypoint file =#
wpfn = os.path.join(outDir, "waypoints.txt")
wptext = os.path.abspath(targMask) + "\n"
wpf = open(wpfn, "w")
wpf.write(wptext)
wpf.close()
check_file(wpfn, logFN=logFN)
cmd = 'probtrackx --mode=seedmask -x %s ' % seedMask + \
'-s %s ' % bedpBase + \
'-m %s ' % brainMask + \
'-l -c 0.2 -S 2000 --steplength=0.5 ' + \
'-P 5000 ' + \
'--forcedir --opd --pd --dir=%s ' % outDir
if targMask != None:
cmd += "--stop=%s --waypoints=%s " % (targMask, wpfn)
fdt_paths_fn = os.path.join(outDir, "fdt_paths.nii.gz")
#== Get the size of fdt_paths.nii.gz. If the size is zero, start over. ==#
if not os.path.isfile(fdt_paths_fn) \
or os.path.getsize(fdt_paths_fn) <= 1 \
or bRedo:
saydo(cmd, logFN=logFN)
#== Check for probtrackx completion ==#
check_file(fdt_paths_fn, logFN=logFN)
#== Save probtrackx command ==#
cmd_fn = os.path.join(outDir, "command.txt")
cmd_f = open(cmd_fn, "wt")
cmd_f.write("%s\n" % cmd)
cmd_f.close()
check_file(cmd_fn, logFN=logFN)
#== Generate seed size-normalized fdt_paths ==#
fdt_paths_norm_fn = os.path.join(outDir, "fdt_paths_norm.nii.gz")
check_bin_path("fslmaths", logFN=logFN)
norm_cmd = "fslmaths -dt float %s -div %d %s -odt float" % \
(fdt_paths_fn, seed_nVoxels, fdt_paths_norm_fn)
if not os.path.isfile(fdt_paths_norm_fn) or bRedo:
saydo(norm_cmd, logFN=logFN)
check_file(fdt_paths_norm_fn, logFN=logFN)
if doSize:
#== Write to seed size file ==#
seed_size_fn = os.path.join(outDir, 'seed_size.txt')
seed_size_f = open(seed_size_fn, 'w')
seed_size_f.write("%d %f" % (int(seed_nVoxels), seed_mm3))
seed_size_f.close()
check_file(seed_size_fn, logFN=logFN)
info_log("INFO: Saved seed size data to file: %s" % seed_size_fn,
logFN=logFN)
if targMask != None:
#== Write to targ size file ==#
targ_size_fn = os.path.join(outDir, 'targ_size.txt')
targ_size_f = open(targ_size_fn, 'w')
targ_size_f.write("%d %f" % (int(targ_nVoxels), targ_mm3))
targ_size_f.close()
check_file(targ_size_fn, logFN=logFN)
info_log("INFO: Saved targ size data to file: %s" % targ_size_fn,
logFN=logFN)
if (targMask != None) and doTargMaskedFDT:
#== Get target masked tract density ==#
check_bin_path("fslstats", logFN=logFN)
(so, se) = cmd_stdout("fslstats %s -k %s -m" \
% (fdt_paths_norm_fn, targMask))
assert (len(se) == 0)
so = so.split()
assert (len(so) >= 1)
targ_masked_norm_fdt = float(so[0])
targ_masked_norm_fdt_fn = \
os.path.join(outDir, "targ_masked_norm_fdt.txt")
tmnff = open(targ_masked_norm_fdt_fn, "wt")
tmnff.write("%f" % targ_masked_norm_fdt)
tmnff.close()
check_file(targ_masked_norm_fdt_fn, logFN=logFN)
info_log("INFO: Saved target-masked normalized FDT value tofile: %s" \
% targ_masked_norm_fdt_fn,
logFN=logFN)
"-overlay %s -fthresh %f -fmid %f " % \
(sigImg, args.fThresh, args.fMid) + \
"-colscalebarflag 1 "
# Prepare the tcl script
tclScript = tempfile.mktemp() + ".tcl"
t_imgFNs = []
t_imgFNs.append(imgFNs["lat"][-1])
t_imgFNs.append(imgFNs["med"][-1])
prep_tcl_script_surf(tclScript, t_imgFNs)
# Put in tcl script information
tksurferCommand += "-tcl %s " % tclScript
# Execute tksurfer
saydo(tksurferCommand)
saydo("rm -rf %s" % tclScript)
for imgFN in t_imgFNs:
check_file(imgFN)
# Stitch images together
# Horizontal stitches
horizStitch = [""] * len(imgFNs.keys())
for (j0, side) in enumerate(imgFNs.keys()):
horizStitch[j0] = tempfile.mktemp() + ".tiff"
stitchCmd = "%s %s %s +append %s" % (CONVERT_BIN,
imgFNs[side][0],
imgFNs[side][1],
horizStitch[j0])
saydo(stitchCmd)
check_file(horizStitch[j0])
def run_probtrackx(seedMask, targMask, bedpBase, brainMask, outDir,
doSeedNorm=True, doSize=True,
doTargMaskedFDT=True,
ccStop=False,
bRedo=False,
logFN=None):
#=========================================================#
# Mode 1: from seed to targ
# Specify both seedMask and targMask
#
# Mode 2: from seed to all
# Specify only seedMask; set targMask=None
#
# Options:
# ccStop: Use corpus callosum stop mask
#
#=========================================================#
import os
from scai_utils import check_file, check_dir, check_bin_path, \
saydo, cmd_stdout, info_log, error_log
from mri_utils import nz_voxels
#== Get seed and targ nvox ==#
check_file(seedMask, logFN=logFN)
(seed_nVoxels, seed_mm3) = nz_voxels(seedMask)
seed_nVoxels = float(seed_nVoxels)
#assert(seed_nVoxels > 0)
if targMask != None:
check_file(targMask, logFN=logFN)
(targ_nVoxels, targ_mm3) = nz_voxels(targMask)
targ_nVoxels = float(targ_nVoxels)
assert(targ_nVoxels > 0)
check_bin_path("probtrackx", logFN=logFN)
check_dir(outDir, logFN=logFN)
if targMask != None:
#= Prepare waypoint file =#
wpfn = os.path.join(outDir, "waypoints.txt")
wptext = os.path.abspath(targMask) + "\n"
wpf = open(wpfn, "w")
wpf.write(wptext)
wpf.close()
check_file(wpfn, logFN=logFN)
cmd = 'probtrackx --mode=seedmask -x %s ' % seedMask + \
'-s %s ' % bedpBase + \
'-m %s ' % brainMask + \
'-l -c 0.2 -S 2000 --steplength=0.5 ' + \
'-P 5000 ' + \
'--forcedir --opd --pd --dir=%s ' % outDir
if targMask != None:
cmd += "--stop=%s --waypoints=%s " % (targMask, wpfn)
fdt_paths_fn = os.path.join(outDir, "fdt_paths.nii.gz")
#== Get the size of fdt_paths.nii.gz. If the size is zero, start over. ==#
if not os.path.isfile(fdt_paths_fn) \
or os.path.getsize(fdt_paths_fn) <= 1 \
or bRedo:
saydo(cmd, logFN=logFN)
#== Check for probtrackx completion ==#
check_file(fdt_paths_fn, logFN=logFN)
#== Save probtrackx command ==#
cmd_fn = os.path.join(outDir, "command.txt")
cmd_f = open(cmd_fn, "wt")
cmd_f.write("%s\n" % cmd)
cmd_f.close()
check_file(cmd_fn, logFN=logFN)
#== Generate seed size-normalized fdt_paths ==#
fdt_paths_norm_fn = os.path.join(outDir, "fdt_paths_norm.nii.gz")
check_bin_path("fslmaths", logFN=logFN)
norm_cmd = "fslmaths -dt float %s -div %d %s -odt float" % \
(fdt_paths_fn, seed_nVoxels, fdt_paths_norm_fn)
if not os.path.isfile(fdt_paths_norm_fn) or bRedo:
saydo(norm_cmd, logFN=logFN)
check_file(fdt_paths_norm_fn, logFN=logFN)
if doSize:
#== Write to seed size file ==#
seed_size_fn = os.path.join(outDir, 'seed_size.txt')
seed_size_f = open(seed_size_fn, 'w')
seed_size_f.write("%d %f" % (int(seed_nVoxels), seed_mm3))
seed_size_f.close()
check_file(seed_size_fn, logFN=logFN)
info_log("INFO: Saved seed size data to file: %s" % seed_size_fn,
logFN=logFN)
if targMask != None:
#== Write to targ size file ==#
targ_size_fn = os.path.join(outDir, 'targ_size.txt')
targ_size_f = open(targ_size_fn, 'w')
targ_size_f.write("%d %f" % (int(targ_nVoxels), targ_mm3))
targ_size_f.close()
check_file(targ_size_fn, logFN=logFN)
info_log("INFO: Saved targ size data to file: %s" % targ_size_fn,
logFN=logFN)
if (targMask != None) and doTargMaskedFDT:
#== Get target masked tract density ==#
check_bin_path("fslstats", logFN=logFN)
(so, se) = cmd_stdout("fslstats %s -k %s -m" \
% (fdt_paths_norm_fn, targMask))
assert(len(se) == 0)
so = so.split()
assert(len(so) >= 1)
targ_masked_norm_fdt = float(so[0])
targ_masked_norm_fdt_fn = \
os.path.join(outDir, "targ_masked_norm_fdt.txt")
tmnff = open(targ_masked_norm_fdt_fn, "wt")
tmnff.write("%f" % targ_masked_norm_fdt)
tmnff.close()
check_file(targ_masked_norm_fdt_fn, logFN=logFN)
info_log("INFO: Saved target-masked normalized FDT value tofile: %s" \
% targ_masked_norm_fdt_fn,
logFN=logFN)
