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 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
raise Exception, "Cannot find any BOLD volumes that match the path wild card: %s" % boldWC
if len(dfs) == nRuns:
info_log("The number of image files matches nRuns. Good")
boldVols = dfs
elif len(dfs) == 2 * nRuns:
info_log("The number of image files equals 2 x nRuns. Assuming that thefirst of each pair os the non-motion corected volume.")
boldVols = dfs[0::2]
else:
raise Exception, "The number of .nii.gz serie in directory %s is neither equal to nRuns=%d or 2*nRuns=%d" % (boldDir, nRuns, 2 * nRuns)
#=== Copy image files and convert them to .nii ===#
niiDir = os.path.join(sBatchDataDir, "nii")
check_dir(niiDir, bCreate=True)
check_bin_path("mri_convert")
niftiFNs = []
for i0 in range(nRuns):
niftiFNs.append(os.path.join(niiDir, "00-%d.nii" % (i0 + 1)))
saydo("mri_convert %s %s" % (boldVols[i0], niftiFNs[-1]))
check_file(niftiFNs[-1])
#=== Determine the number of contrasts ===#
contr = loadmat(contrMat)
nContrasts = len(contr["RegNameTContrasts"][0])
info_log("Number of contrasts = %d" % nContrasts)
#=== Check for the FS subject data dir ===#
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)
help="Functional activation (sig) threshold (e.g., 3)")
ap.add_argument("fMid", type=float,
help="Functional activation (sig) mid value (e.g., 5)")
if len(sys.argv) == 1:
ap.print_help()
sys.exit(1)
args = ap.parse_args()
if args.type == "both":
types = ["sf10", "vol"]
else:
types = [args.type]
check_bin_path(CONVERT_BIN)
check_dir(CON_IMG_DIR)
l2Base = os.path.abspath(L2_BATCH_BASE)
check_dir(l2Base)
stitchRes = {}
for t_type in types:
conDir = os.path.join(l2Base,
"%s_%s_%s" % (args.grp, args.contr, t_type))
check_dir(conDir)
stitchRes[t_type] = {}
if t_type.startswith("sf"):
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)