import os
import sys
import argparse
from scai_utils import *
"""
speechROIs = ['H', 'PO', 'PP', 'PT', 'SPL', 'TP', 'SMA', 'aCG', 'aCO', \
'aFO', 'aINS', 'aSTg', 'adSTs', \
'aSMg', 'dIFo', 'dMC', 'dSC', 'mdPMC', 'midMC', 'midPMC', 'pCO', \
'pFO', 'pIFs', 'pINS', 'aSTg', 'pSTg', 'pdPMC', 'pdSTs', \
'preSMA', 'vIFo', 'vMC', 'vPMC', 'vSC', 'midCG']
"""
from aparc12_oldVer import get_aparc12_cort_rois
speechROIs = get_aparc12_cort_rois("all", bSpeech=True)
#speechROIs = ['midCG']
BIN = "/users/cais/STUT/scripts/aparc12_probtrackx_2.py"
RES_DIR = "/users/cais/STUT/analysis/aparc12_tracts_pt2"
if __name__ == "__main__":
ap = argparse.ArgumentParser(description="Run aparc12_probtrackx_2.py under seedOnly, caww (corpus-callosum avoidance, ipsilateral WM waypoint) mode on all speech-network ROIs of a hemisphere of a subject")
ap.add_argument("sID", help="Subject ID")
ap.add_argument("hemi", help="Hemisphere (e.g., lh or lh,rh)")
ap.add_argument("--noSurfProj", dest="bNoSurfProj", action="store_true", \
help="Do not perform projection to surface")
ap.add_argument("--redo", dest="bRedo", action="store_true", \
help="Force redo all ROIs. If False, then the script will skip the ROIs that have already been completed.")
if bpt2:
TRACTS_RES_DIR = TRACTS_RES_DIR_PT2
check_dir(TRACTS_RES_DIR)
# Check sanity of input arguments
if not (hemi == "lh" or hemi == "rh" or hemi == "xh"):
raise Exception, "Unrecognized hemisphere: %s" % hemi
if len(speechMode) > 6:
if hemi != speechMode_noThr[-2 :]:
raise Exception, "Mismatch between hemi=%s and speechMode=%s" \
% (hemi, speechMode)
# Read cortical ROI list
if speechMode == "speech":
t_rois = get_aparc12_cort_rois("all", bSpeech=True)
else:
t_rois = get_aparc12_cort_rois("all", bSpeech=speechMode)
t_rois.sort()
h_rois = []
if hemi == "lh" or hemi == "rh":
for t_roi in t_rois:
h_rois.append(hemi + "_" + t_roi)
elif hemi == "xh":
hemis = ["lh", "rh"]
for t_hemi in hemis:
for t_roi in t_rois:
h_rois.append(t_hemi + "_" + t_roi)
# Preparation: check directories
args = ap.parse_args()
if args.bOldVer:
from aparc12_oldVer import get_aparc12_cort_rois
else:
from aparc12 import get_aparc12_cort_rois
check_dir(FSAV_DIR)
check_file(APARC12_VOL)
check_file(APARC12_CTAB)
# Read color table
(roi_nums, roi_names) = read_ctab(APARC12_CTAB)
# Get the set of ROIs to process
proc_rois_0 = get_aparc12_cort_rois(bSpeech=False)
# Duplex the rois in to both hemispheres and get their numbers
proc_roi_names = []
proc_roi_nums = []
for (i0, themi) in enumerate(hemis):
for (i1, troi) in enumerate(proc_rois_0):
troi_name = themi + "_" + troi
proc_roi_names.append(troi_name)
if roi_names.count(troi_name) == 0:
raise Exception, "Cannot find ROI %s in color table %s" \
% (troi_name, APARC12_CTAB)
proc_roi_nums.append(roi_nums[roi_names.index(troi_name)])
