#!/usr/bin/python
import os
import sys
import glob
import argparse
from aparc12 import get_aparc12_cort_rois
from scai_utils import *
tractSegDir = "/users/cais/STUT/analysis/tractseg_aparc12/"
L2_DIR = "/users/cais/STUT/analysis/tract_subcort_conn"
allROIs = get_aparc12_cort_rois(lobe="all", bSpeech=False)
allROIs.sort()
if __name__ == "__main__":
ap = argparse.ArgumentParser(description="Batch run of tractography- and aparc12-based subcorticla-cortical connectivity analysis, by calling tract_seg.py and tract_subcort_conn.py")
ap.add_argument("scSeed", \
help="Subcortical seed (e.g., lh.Thalamus-Proper)")
if len(sys.argv) == 1:
ap.print_help()
sys.exit(0)
args = ap.parse_args()
check_dir(tractSegDir)
ds = glob.glob(os.path.join(tractSegDir, "S??"))
ds.sort()
if len(sys.argv) == 1:
ap.print_help()
sys.exit(0)
# === Parse input arguments === #
args = ap.parse_args()
inMatFN = args.inMatFN
hemi = args.hemi
grp = args.grp
vmax = args.vmax
# === ROIs by lobe ===
rois_bl = {}
for (i0, t_lobe) in enumerate(lobes):
rois_bl[t_lobe] = get_aparc12_cort_rois(lobe=t_lobe, bSpeech=True)
rois_bl[t_lobe] = np.array(rois_bl[t_lobe])
# === Read the ROI centers of gravity from text file === #
# check_file(COORD_FILE)
cf = open(COORD_FILE, "rt")
ct = cf.read().split('\n')
ct = remove_empty_strings(ct)
cf.close()
roi_names = []
roi_nums = []
roi_coords = []
for (i0, tline) in enumerate(ct):
t_items = tline.split(' ')
regionCodes = [1, 2, 3, 4, 5, 6, 7]
"""
regionROIs = [['SFg', 'aMFg', 'iFo', 'iFt', 'FMC', 'FO', 'FOC', 'FP', \
'pMFg'], \
['pSMA', 'aSMA', 'adPMC', 'mdPMC', 'pdPMC', 'vPMC'], \
['aCO', 'vMC', 'dMC'], \
['vSSC', 'pCO', 'dSSC'], \
['AG', 'aSMg', 'pSMg', 'SPL'], \
['CALC', 'MTO', 'ITO'], \
['H', 'PT', 'aSTg', 'aMTg', 'aITg', 'pSTg', 'pMTg', 'pITg', \
'TP', 'adSTs', 'avSTs', 'pdSTs', 'pvSTs'],\
]
"""
regionROIs = [[]] * len(regions)
for (i0, region) in enumerate(regions):
regionROIs[i0] = get_aparc12_cort_rois(lobe=region, bSpeech=False)
allROIs = get_aparc12_cort_rois(lobe="all", bSpeech=False)
altROINames = {"orig": ["Ag", "Hg", "Lg", "ITOg", "MTOg", \
"aCGg", "midCGg", "pCGg", "aPHg", "pPHg"], \
"alt": ["AG", "H", "LG", "ITO", "MTO", \
"aCG", "midCG", "pCG", "aPH", "pPH"]}
# ==== ~CONFIG: Construct the parcellation profile ==== #
# ==== sub_routine ==== #
def tract_seg_sub(args, step, roiName=""):
# Check input arguments
sID = args.sID
# Check sanity of input arguments
if not (hemi == "lh" or hemi == "rh"):
raise Exception, "Unrecognized hemisphere: %s" % hemi
if segType.count("-") == 1:
segType1 = segType.replace("-", "_")
if SEG_TYPE_NUMSEGS.keys().count(segType1) != 1:
raise Exception, "Unrecognized segType: %s" % segType1
nSegs = SEG_TYPE_NUMSEGS[segType1]
else:
if SEG_TYPE_NUMSEGS.keys().count(segType) != 1:
raise Exception, "Unrecognized segType: %s" % segType
nSegs = SEG_TYPE_NUMSEGS[segType]
# Read cortical ROI list
t_rois = list(get_aparc12_cort_rois(bSpeech=bSpeech))
t_rois.sort()
h_rois = []
for t_roi in t_rois:
h_rois.append(hemi + "_" + t_roi)
# Preparation: check directories
sDataDir = os.path.join(DATA_DIR, sID)
check_dir(sDataDir)
sTracDir = os.path.join(TRACULA_BASE, sID)
check_dir(sTracDir)
sResDir = os.path.join(TRACTS_RES_DIR, sID)
check_dir(sResDir)
