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compute_css_derivatives.py
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"""
-----------------------------------------------------------------------------------------
compute_css_derivatives.py
-----------------------------------------------------------------------------------------
Goal of the script:
Compute pRF derivatives from the pRF grid gauss fit
-----------------------------------------------------------------------------------------
Input(s):
sys.argv[1]: main project directory
sys.argv[2]: project name (correspond to directory)
sys.argv[3]: subject name (e.g. sub-01)
sys.argv[4]: group (e.g. 327)
-----------------------------------------------------------------------------------------
Output(s):
Combined estimate nifti file and pRF derivative nifti file
-----------------------------------------------------------------------------------------
To run:
1. cd to function
>> cd ~/projects/[PROJECT]/analysis_code/postproc/prf/postfit/
2. run python command
>> python compute_css_derivatives.py [main directory] [project name] [subject num] [group]
-----------------------------------------------------------------------------------------
Exemple:
cd ~/projects/pRF_analysis/analysis_code/postproc/prf/postfit/
python compute_css_derivatives.py /scratch/mszinte/data MotConf sub-01 327
python compute_css_derivatives.py /scratch/mszinte/data MotConf sub-170k 327
python compute_css_derivatives.py /scratch/mszinte/data RetinoMaps sub-01 327
python compute_css_derivatives.py /scratch/mszinte/data RetinoMaps sub-170k 327
python compute_css_derivatives.py /scratch/mszinte/data amblyo_prf sub-01 327
python compute_css_derivatives.py /scratch/mszinte/data amblyo_prf sub-170k 327
-----------------------------------------------------------------------------------------
Written by Martin Szinte ([email protected])
and Uriel Lascombes ([email protected])
-----------------------------------------------------------------------------------------
"""
# Stop warnings
import warnings
warnings.filterwarnings("ignore")
# Debug
import ipdb
deb = ipdb.set_trace
# General imports
import os
import re
import sys
import glob
import json
import numpy as np
import nibabel as nb
# Personal imports
sys.path.append("{}/../../../utils".format(os.getcwd()))
from prf_utils import fit2deriv
from maths_utils import median_subject_template
from surface_utils import make_surface_image , load_surface
from pycortex_utils import set_pycortex_config_file
# Inputs
main_dir = sys.argv[1]
project_dir = sys.argv[2]
subject = sys.argv[3]
group = sys.argv[4]
# Load settings
base_dir = os.path.abspath(os.path.join(os.getcwd(), "../../../../"))
settings_path = os.path.join(base_dir, project_dir, "settings.json")
with open(settings_path) as f:
json_s = f.read()
analysis_info = json.loads(json_s)
formats = analysis_info['formats']
extensions = analysis_info['extensions']
rois = analysis_info['rois']
maps_names = analysis_info['maps_names_css']
subjects = analysis_info['subjects']
prf_task_name = analysis_info['prf_task_name']
# Set pycortex db and colormaps
cortex_dir = "{}/{}/derivatives/pp_data/cortex".format(main_dir, project_dir)
set_pycortex_config_file(cortex_dir)
# Define folders
pp_dir = "{}/{}/derivatives/pp_data".format(main_dir, project_dir)
# sub-170k exception
if subject != 'sub-170k':
for format_, extension in zip(formats, extensions):
print(format_)
# Define directories
prf_deriv_dir = "{}/{}/{}/prf/prf_derivatives".format(pp_dir, subject, format_)
os.makedirs(prf_deriv_dir, exist_ok=True)
# Get prf fit filenames
fit_fns = glob.glob("{}/{}/{}/prf/fit/*prf-fit_css*.{}".format(
pp_dir, subject, format_, extension))
# Compute derivatives
for fit_fn in fit_fns:
deriv_fn = fit_fn.split('/')[-1].replace('prf-fit', 'prf-deriv')
if os.path.isfile(fit_fn) == False:
sys.exit('Missing files, analysis stopped : {}'.format(fit_fn))
else:
# get arrays
fit_img, fit_data = load_surface(fit_fn)
deriv_array = fit2deriv(fit_array=fit_data, model='css', is_loo_r2=True)
deriv_img = make_surface_image(data=deriv_array,
source_img=fit_img,
maps_names=maps_names)
nb.save(deriv_img,'{}/{}'.format(prf_deriv_dir, deriv_fn))
print('Saving derivatives: {}'.format('{}/{}'.format(prf_deriv_dir, deriv_fn)))
# Find all the derivatives files
derives_fns = []
for format_, extension in zip(formats, extensions):
list_ = glob.glob("{}/{}/{}/prf/prf_derivatives/*loo-*_prf-deriv_css.{}".format(
pp_dir, subject, format_, extension))
derives_fns.extend(list_)
# Split filtered files depending of their nature
deriv_fsnative_hemi_L, deriv_fsnative_hemi_R, deriv_170k = [], [], []
for subtype in derives_fns:
if "hemi-L" in subtype: deriv_fsnative_hemi_L.append(subtype)
elif "hemi-R" in subtype: deriv_fsnative_hemi_R.append(subtype)
else : deriv_170k.append(subtype)
loo_deriv_fns_list = [deriv_fsnative_hemi_L,
deriv_fsnative_hemi_R,
deriv_170k]
hemi_data_median = {'hemi-L': [],
'hemi-R': [],
'170k': []}
# Median
print('Compute median across LOO')
for loo_deriv_fns in loo_deriv_fns_list:
if loo_deriv_fns[0].find('hemi-L') != -1: hemi = 'hemi-L'
elif loo_deriv_fns[0].find('hemi-R') != -1: hemi = 'hemi-R'
else: hemi = None
deriv_img, deriv_data = load_surface(fn=loo_deriv_fns[0])
loo_deriv_data_median = np.zeros(deriv_data.shape)
for n_run, loo_deriv_fn in enumerate(loo_deriv_fns):
loo_deriv_median_fn = loo_deriv_fn.split('/')[-1]
loo_deriv_median_fn = re.sub(r'avg_loo-\d+_prf-deriv_css', 'avg_prf-deriv_css_loo-median', loo_deriv_median_fn)
# Load data
print('adding {} to computing median'.format(loo_deriv_fn))
loo_deriv_img, loo_deriv_data = load_surface(fn=loo_deriv_fn)
# Median
if n_run == 0: loo_deriv_data_median = np.copy(loo_deriv_data)
else: loo_deriv_data_median = np.nanmedian(np.array([loo_deriv_data_median, loo_deriv_data]), axis=0)
if hemi:
median_fn = '{}/{}/fsnative/prf/prf_derivatives/{}'.format(
pp_dir, subject, loo_deriv_median_fn)
hemi_data_median[hemi] = loo_deriv_data_median
else:
median_fn = '{}/{}/170k/prf/prf_derivatives/{}'.format(
pp_dir, subject, loo_deriv_median_fn)
hemi_data_median['170k'] = loo_deriv_data_median
# Export data in surface format
loo_deriv_img = make_surface_image(data=loo_deriv_data_median,
source_img=loo_deriv_img,
maps_names=maps_names)
nb.save(loo_deriv_img, median_fn)
print('Saving median: {}'.format(median_fn))
# Sub-170k computing median
elif subject == 'sub-170k':
print('sub-170, computing median prf deriv across subject...')
# find all the subject prf derivatives
subjects_derivatives = []
for subject in subjects:
subjects_derivatives += ["{}/{}/derivatives/pp_data/{}/170k/prf/prf_derivatives/{}_task-{}_fmriprep_dct_avg_prf-deriv_css_loo-median.dtseries.nii".format(
main_dir, project_dir, subject, subject, prf_task_name)]
# Computing median across subject
img, data_deriv_median = median_subject_template(fns=subjects_derivatives)
# Export results
sub_170k_deriv_dir = "{}/{}/derivatives/pp_data/sub-170k/170k/prf/prf_derivatives".format(
main_dir, project_dir)
os.makedirs(sub_170k_deriv_dir, exist_ok=True)
sub_170k_deriv_fn = "{}/sub-170k_task-{}_fmriprep_dct_avg_prf-deriv_css_loo-median.dtseries.nii".format(sub_170k_deriv_dir, prf_task_name)
print("save: {}".format(sub_170k_deriv_fn))
sub_170k_deriv_img = make_surface_image(data=data_deriv_median,
source_img=img,
maps_names=maps_names)
nb.save(sub_170k_deriv_img, sub_170k_deriv_fn)
# Define permission cmd
print('Changing files permissions in {}/{}'.format(main_dir, project_dir))
os.system("chmod -Rf 771 {}/{}".format(main_dir, project_dir))
os.system("chgrp -Rf {} {}/{}".format(group, main_dir, project_dir))