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dicomfunction_rest.py
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# input is config file (old or new)
# get:
# subject's name for dicom folder
# numbered ordering of all the runs
# output: subject name folder-ses01, with all the dicom folders in that structure
# PennCfg: will tell you which dicoms will go with functional scans
def transferdicoms(subject,day):
print('transferring dicom files for subject %i, day %i' % (subject,day))
from rtfMRI.RtfMRIClient import RtfMRIClient, loadConfigFile
from shutil import copyfile
import numpy as np
import datetime
import glob
import os
import shutil
import sys
exp_dir = "/data/jux/cnds/amennen/rtAttenPenn/fmridata/behavdata/gonogo/"
exp = exp_dir + 'subject' + str(subject) + '/usedscripts/PennCfg_Day' + str(day) + '.toml'
cfg=loadConfigFile(exp)
# add check here that subject name matches!! ###
subjectName=cfg.session.subjectName
subjectNum=cfg.session.subjectNum
if subjectNum is not subject:
raise ValueError('Subject number does not agree with cfg file')
subjectDay=cfg.session.subjectDay
if subjectDay is not day:
raise ValueError('Day number does not agree with cfg file')
if subjectDay==1:
allRuns=np.array(cfg.session.Runs1)
allScans=np.array(cfg.session.ScanNums1)
elif subjectDay==2:
allRuns=np.array(cfg.session.Runs2)
allScans=np.array(cfg.session.ScanNums2)
elif subjectDay==3:
allRuns=np.array(cfg.session.Runs3)
allScans=np.array(cfg.session.ScanNums3)
dicom_dir="/data/jux/cnds/amennen/rtAttenPenn/fmridata/transferredImages"
dt = datetime.datetime.strptime(cfg.session.subjectName[0:6], "%m%d%y")
dicom_folder=dicom_dir + "/" + datetime.datetime.strftime(dt,"%Y%m%d") + "." + subjectName + "." + subjectName
print('loading from %s' % dicom_folder)
# we know what the numbers were for the functional runs onwards
SCAN_NUMBERS= {}
nRuns = len(allRuns)
for r in np.arange(nRuns):
runNumber = r + 1
SCAN_NUMBERS['gonogo%i' % runNumber] = allScans[r]-1 # important: both moco and non-moco versions
#dayorder={}
#day1order=['scout', 'T1w', 'faces1', 'faces2', 'gonogo1', 'gonogo2', 'gonogo3', 'gonogo4', 'gonogo5', 'gonogo6', 'gonogo7', 'fmap1', 'fmap2']
allfunc={}
allfunc[1]=['rest', 'faces1', 'faces2', 'gonogo1', 'gonogo2', 'gonogo3', 'gonogo4', 'gonogo5', 'gonogo6', 'gonogo7']
allfunc[2]=['exfunc', 'gonogo1', 'gonogo2', 'gonogo3', 'gonogo4', 'gonogo5', 'gonogo6', 'gonogo7', 'gonogo8', 'gonogo9']
allfunc[3]=['exfunc','gonogo1', 'gonogo2', 'gonogo3', 'gonogo4', 'gonogo5', 'gonogo6', 'gonogo7', 'gonogo8','faces1', 'faces2', 'rest' ]
anat=['scout', 'T1w']
fmap=['fmap1', 'fmap2']
last_scan = glob.glob(dicom_folder + "/*.dcm")[-1]
last_run = int(last_scan[-17:-11])
DICOM_DICT = {}
NDICOM = {}
for s_ind in np.arange(last_run):
this_runs_dicom = glob.glob(dicom_folder + "/001_%6.6i*.dcm" % (s_ind+1))
DICOM_DICT[s_ind+1] = this_runs_dicom
NDICOM[s_ind+1] = len(this_runs_dicom)
print("FOUND: scanning run %i contains %i dicom files" %(s_ind+1,len(this_runs_dicom)))
scout_begin_TR=128
faces_TR=147
gonogo_TR=242
fmap1_TR=120
fmap2_TR=60
exfunc_TR=10
anat_TR=176
rest_TR=190
anat = [key for key,val in NDICOM.items() if val==anat_TR]
scout1 = [key for key,val in NDICOM.items() if val==scout_begin_TR][0]
faces = [key for key,val in NDICOM.items() if val==faces_TR]
fmap1 = [key for key,val in NDICOM.items() if val==fmap1_TR]
fmap2 = [key for key,val in NDICOM.items() if val==fmap2_TR]
exfunc = [key for key,val in NDICOM.items() if val==exfunc_TR]
rest = [key for key,val in NDICOM.items() if val==rest_TR]
SCAN_NUMBERS['scout'] = np.arange(scout1,scout1+4)
if len(anat)>0:
SCAN_NUMBERS['T1w'] = anat[0]
ANAT_TAKEN = True
else:
ANAT_TAKEN = False
if len(faces) > 0:
SCAN_NUMBERS['faces1'] = faces[0]
SCAN_NUMBERS['faces2'] = faces[2]
if len(exfunc) > 0:
SCAN_NUMBERS['exfunc'] = exfunc[0]
if len(rest) > 0:
SCAN_NUMBERS['rest'] = rest[0]
SCAN_NUMBERS['fmap1'] = fmap1[0]
SCAN_NUMBERS['fmap2'] = fmap2[0]
############################################################################################
# CHECK ALL THE SCAN NUMBERS ARE CORRECT
############################################################################################
print('*******************************')
print('scan numbers are')
for k, v in SCAN_NUMBERS.items():
print(k, v)
correct_scans = input('Are the scan numbers correct?y/n\n')
if correct_scans == 'n':
sys.exit('wrong scan numbers!\n MODIFY THEM IN %s' % exp )
############################################################################################
# CHECK ALL THE SCAN NUMBERS ARE CORRECT
############################################################################################
# now we can iterate over the whole folder and copy the dicom files over into new directory
dicom_out="/data/jux/cnds/amennen/rtAttenPenn/fmridata/Dicom"
bids_id = 'sub-{0:03d}'.format(subjectNum)
ses_id = 'ses-{0:02d}'.format(subjectDay)
day_path=os.path.join(dicom_out,bids_id,ses_id)
# now make each directory for type of scan
if ANAT_TAKEN:
scantypes=['anat', 'fmap', 'func']
else:
scantypes=['fmap', 'func']
for s in scantypes:
full_path=os.path.join(day_path,s)
if not os.path.exists(full_path):
os.makedirs(full_path)
# start with scout
#src_files = DICOM_DICT[SCAN_NUMBERS['scout']]
#dest_path = os.path.join(day_path,'anat','scout')
#if not os.path.exists(dest_path):
# os.makedirs(dest_path)
#for file_name in src_files:
# fn=os.path.split(file_name)[-1]
# dest=os.path.join(dest_path,fn)
# shutil.copyfile(file_name, dest)
# first transfer anat
if ANAT_TAKEN:
src_files = DICOM_DICT[SCAN_NUMBERS['T1w']]
dest_path = os.path.join(day_path,'anat', 'T1w')
exfile=os.path.split(src_files[0])[-1]
print('copying run from %s into %s' % (exfile,dest_path))
if not os.path.exists(dest_path):
os.makedirs(dest_path)
for file_name in src_files:
fn=os.path.split(file_name)[-1]
dest=os.path.join(dest_path,fn)
shutil.copyfile(file_name, dest)
dest_path = os.path.join(day_path, 'func')
n_func_scans = len(allfunc[subjectDay])
scan_names=allfunc[subjectDay]
nrunsperfunc = 2
faces_counter=0
gonogo_counter=0
for f_ind in np.arange(n_func_scans):
this_scan=scan_names[f_ind]
if 'faces' in this_scan:
task='faces'
faces_counter+=1
run=faces_counter
elif 'gonogo' in this_scan:
task='gonogo'
gonogo_counter+=1
run=gonogo_counter
elif 'exfunc' in this_scan:
task='exfunc'
run=1
elif 'rest' in this_scan:
task='rest'
run=1
full_name= 'task-' + task + '_' + 'rec-' + 'uncorrected' + '_' + 'run-{0:02d}'.format(run) + '_bold'
dicom_out=os.path.join(dest_path,full_name)
if not os.path.exists(dicom_out):
os.makedirs(dicom_out)
src_files = DICOM_DICT[SCAN_NUMBERS[this_scan]]
exfile=os.path.split(src_files[0])[-1]
print('copying run from %s into %s' % (exfile,dicom_out))
for file_name in src_files:
fn=os.path.split(file_name)[-1]
dest = os.path.join(dicom_out,fn)
shutil.copyfile(file_name, dest)
# full_name= 'task-' + task + '_' + 'rec-' + 'corrected' + '_' + 'run-{0:02d}'.format(run) + '_bold'
# dicom_out=os.path.join(dest_path,full_name)
# if not os.path.exists(dicom_out):
# os.makedirs(dicom_out)
# src_files = DICOM_DICT[SCAN_NUMBERS[this_scan] + 1]
# exfile=os.path.split(src_files[0])[-1]
# print('copying run from %s into %s' % (exfile,dicom_out))
# for file_name in src_files:
# fn=os.path.split(file_name)[-1]
# dest = os.path.join(dicom_out,fn)
# shutil.copyfile(file_name, dest)
# now do same for fmap
this_scan='fmap1'
# first scan is magnitude
dest_path = os.path.join(day_path,'fmap')
full_name='magnitude1'
dicom_out=os.path.join(dest_path,full_name)
if not os.path.exists(dicom_out):
os.makedirs(dicom_out)
src_files = DICOM_DICT[SCAN_NUMBERS[this_scan]]
exfile=os.path.split(src_files[0])[-1]
print('copying run from %s into %s' % (exfile,dicom_out))
for file_name in src_files:
fn=os.path.split(file_name)[-1]
dest = os.path.join(dicom_out,fn)
shutil.copyfile(file_name, dest)
this_scan='fmap2'
dest_path = os.path.join(day_path,'fmap')
full_name='phasediff'
dicom_out=os.path.join(dest_path,full_name)
if not os.path.exists(dicom_out):
os.makedirs(dicom_out)
src_files = DICOM_DICT[SCAN_NUMBERS[this_scan]]
exfile=os.path.split(src_files[0])[-1]
print('copying run from %s into %s' % (exfile,dicom_out))
for file_name in src_files:
fn=os.path.split(file_name)[-1]
dest = os.path.join(dicom_out,fn)
shutil.copyfile(file_name, dest)