def get_hue_selectivity(prf_dir, db_dir, subj_id, roi):
"""Get hue tunning curve for each voxel and calculate hue selectivity."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# pRF estimate
roi_dir = os.path.join(prf_dir, roi)
sel_paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model_corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
hue_tunes = np.zeros((len(vxl_idx), 201))
hue_sel = np.zeros(len(vxl_idx))
for i in range(len(vxl_idx)):
print 'Voxel %s, Val Corr %s' % (i, sel_model_corr[i])
paras = sel_paras[i]
# get hue selection
hue_tunes[i] = para2hue(paras[40:])
hue_sel[i] = abs(hue_tunes[i].max() - hue_tunes[i].min())
if sel_model_corr[i] >= 0.25:
hue_file = os.path.join(
roi_dir, 'Voxel_%s_%s_hue.png' % (i + 1, vxl_idx[i]))
vutil.save_hue(hue_tunes[i], hue_file)
np.save(os.path.join(roi_dir, 'hue_tunes.npy'), hue_tunes)
np.save(os.path.join(roi_dir, 'hue_selectivity.npy'), hue_sel)
def get_prediction_residual(prf_dir, db_dir, subj_id):
roi_list = ['v1rh', 'v1lh', 'v2rh', 'v2lh', 'v3rh', 'v3lh', 'v4rh', 'v4lh']
orig_fmri = None
pred_fmri = None
res_fmri = None
vxl_idx = None
for roi in roi_list:
idx, tx, vx = dataio.load_vim2_fmri(db_dir, subj_id, roi)
m = tx.mean(axis=1, keepdims=True)
s = tx.std(axis=1, keepdims=True)
roi_pred_file = os.path.join(prf_dir, roi, 'train_pred_norm_fmri.npy')
roi_pred_fmri = np.load(roi_pred_file)
roi_pred_fmri = roi_pred_fmri * s + m
res = tx - roi_pred_fmri
if not isinstance(res_fmri, np.ndarray):
orig_fmri = tx
pred_fmri = roi_pred_fmri
res_fmri = res
vxl_idx = idx
else:
orig_fmri = np.vstack((orig_fmri, tx))
pred_fmri = np.vstack((pred_fmri, roi_pred_fmri))
res_fmri = np.vstack((res_fmri, res))
vxl_idx = np.concatenate((vxl_idx, idx))
outfile = os.path.join(prf_dir, 'roi_coding_fmri')
np.savez(outfile,
orig_fmri=orig_fmri,
pred_fmri=pred_fmri,
res_fmri=res_fmri,
vxl_idx=vxl_idx)
def gabor_contribution2prf(feat_dir, prf_dir, db_dir, subj_id, roi):
"""Calculate tunning contribution of each gabor sub-banks."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
val_models = np.load(os.path.join(feat_dir, 'val_candidate_model.npy'),
mmap_mode='r')
# load selected model parameters
roi_dir = os.path.join(prf_dir, roi)
paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
gabor_corr = np.zeros((paras.shape[0], 5))
for i in range(paras.shape[0]):
print 'Voxel %s' % (i)
# load features
feats = np.array(val_models[int(sel_model[i]), ...]).astype(np.float64)
feats = zscore(feats).T
for j in range(5):
pred = np.dot(feats[:, (j * 8):(j * 8 + 8)],
paras[i, (j * 8):(j * 8 + 8)])
gabor_corr[i, j] = np.corrcoef(pred, val_fmri_ts[i])[0, 1]
np.save(os.path.join(roi_dir, 'gabor_contributes.npy'), gabor_corr)
def stimuli_recon(prf_dir, db_dir, subj_id, roi):
"""Reconstruct stimulus based on pRF model."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load model parameters
roi_dir = os.path.join(prf_dir, roi)
val_corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
filters = np.load(os.path.join(roi_dir, 'filters.npy'))
recon_imgs = np.zeros((val_fmri_ts.shape[1], 128, 128))
# fMRI data z-score
print 'fmri data temporal z-score'
m = np.mean(val_fmri_ts, axis=1, keepdims=True)
s = np.std(val_fmri_ts, axis=1, keepdims=True)
val_fmri_ts = (val_fmri_ts - m) / (1e-10 + s)
# select significant predicted voxels
sel_vxls = np.nonzero(val_corr >= 0.17)[0]
for i in range(val_fmri_ts.shape[1]):
print 'Reconstruct stimilus %s' % (i + 1)
tmp = np.zeros((128, 128))
for j in sel_vxls:
tmp += val_fmri_ts[int(j), int(i)] * filters[j]
recon_imgs[i] = tmp
np.save(os.path.join(roi_dir, 'recon_img.npy'), recon_imgs)
def null_distribution_prf_tunning(feat_dir, prf_dir, db_dir, subj_id, roi):
"""Generate Null distribution of pRF model tunning using validation data."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
val_models = np.load(os.path.join(feat_dir, 'val_candidate_model.npy'),
mmap_mode='r')
# output directory config
roi_dir = os.path.join(prf_dir, roi)
# load selected model parameters
paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
null_corr = np.zeros((paras.shape[0], 1000))
for i in range(paras.shape[0]):
print 'Voxel %s' % (i)
# load features
feats = np.array(val_models[int(sel_model[i]), ...]).astype(np.float64)
feats = zscore(feats).T
pred = np.dot(feats, paras[i])
for j in range(1000):
shuffled_val_ts = np.random.permutation(val_fmri_ts[i])
null_corr[i, j] = np.corrcoef(pred, shuffled_val_ts)[0, 1]
np.save(os.path.join(roi_dir, 'random_corr.npy'), null_corr)
def prf_selection(feat_dir, prf_dir, db_dir, subj_id, roi):
"""Select best model for each voxel and validating."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
val_models = np.load(os.path.join(feat_dir, 'val_candidate_model.npy'),
mmap_mode='r')
# output directory config
roi_dir = os.path.join(prf_dir, roi)
# load candidate model parameters
paras = np.load(os.path.join(roi_dir, 'reg_paras.npy'))
mcorr = np.load(os.path.join(roi_dir, 'reg_model_corr.npy'))
alphas = np.load(os.path.join(roi_dir, 'reg_alphas.npy'))
sel_paras = np.zeros((mcorr.shape[1], 46))
sel_model = np.zeros(mcorr.shape[1])
sel_model_corr = np.zeros(mcorr.shape[1])
for i in range(mcorr.shape[1]):
maxi = np.argmax(mcorr[:, i])
print 'Voxel %s - Max corr %s - Model %s' % (i, mcorr[maxi, i], maxi)
print 'Alpha : %s' % (alphas[maxi, i])
sel_paras[i] = paras[maxi, i]
sel_model[i] = maxi
feats = np.array(val_models[maxi, ...]).astype(np.float64)
feats = zscore(feats).T
pred = np.dot(feats, sel_paras[i])
sel_model_corr[i] = np.corrcoef(pred, val_fmri_ts[i])[0, 1]
print 'Val Corr : %s' % (sel_model_corr[i])
np.save(os.path.join(roi_dir, 'reg_sel_paras.npy'), sel_paras)
np.save(os.path.join(roi_dir, 'reg_sel_model.npy'), sel_model)
np.save(os.path.join(roi_dir, 'reg_sel_model_corr.npy'), sel_model_corr)
def filter_recon(prf_dir, db_dir, subj_id, roi):
"""Reconstruct filter map of each voxel based on selected model."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# output config
roi_dir = os.path.join(prf_dir, roi)
# pRF estimate
sel_models = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
sel_paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model_corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
filters = np.zeros((sel_models.shape[0], 128, 128))
fig_dir = os.path.join(roi_dir, 'filters')
check_path(fig_dir)
thr = 0.17
# gabor bank generation
gwt = bob.ip.gabor.Transform()
gwt.generate_wavelets(128, 128)
spatial_gabors = np.zeros((40, 128, 128))
for i in range(40):
w = bob.ip.gabor.Wavelet(resolution=(128, 128),
frequency=gwt.wavelet_frequencies[i])
sw = bob.sp.ifft(w.wavelet.astype(np.complex128))
spatial_gabors[i, ...] = np.roll(np.roll(np.real(sw), 64, 0), 64, 1)
for i in range(sel_models.shape[0]):
if sel_model_corr[i] < thr:
continue
print 'Voxel %s, Val Corr %s' % (i, sel_model_corr[i])
model_idx = int(sel_models[i])
# get gaussian pooling field parameters
si = model_idx / 1024
xi = (model_idx % 1024) / 32
yi = (model_idx % 1024) % 32
x0 = np.arange(0, 128, 4)[xi]
y0 = np.arange(0, 128, 4)[yi]
s = np.linspace(1, 50, 15)[si]
kernel = make_2d_gaussian(128, s, center=(x0, y0))
kpos = np.nonzero(kernel)
paras = sel_paras[i]
for gwt_idx in range(40):
wt = paras[gwt_idx]
arsw = spatial_gabors[gwt_idx]
for p in range(kpos[0].shape[0]):
tmp = img_offset(arsw, (kpos[0][p], kpos[1][p]))
filters[i] += wt * kernel[kpos[0][p], kpos[1][p]] * tmp
if sel_model_corr[i] >= thr:
im_file = os.path.join(fig_dir,
'Voxel_%s_%s.png' % (i + 1, vxl_idx[i]))
vutil.save_imshow(filters[i], im_file)
np.save(os.path.join(roi_dir, 'filters.npy'), filters)
def merge_roi_data(prf_dir, db_dir, subj_id):
roi_list = ['v1rh', 'v1lh', 'v2rh', 'v2lh', 'v3rh', 'v3lh', 'v4rh', 'v4lh']
train_ts = None
val_ts = None
vxl_idx = None
for roi in roi_list:
idx, tx, vx = dataio.load_vim2_fmri(db_dir, subj_id, roi)
if not isinstance(train_ts, np.ndarray):
train_ts = tx
val_ts = vx
vxl_idx = idx
else:
train_ts = np.vstack((train_ts, tx))
val_ts = np.vstack((val_ts, vx))
vxl_idx = np.concatenate((vxl_idx, idx))
outfile = os.path.join(prf_dir, 'roi_orig_fmri')
np.savez(outfile, train_ts=train_ts, val_ts=val_ts, vxl_idx=vxl_idx)
def prf_recon(prf_dir, db_dir, subj_id, roi):
"""Reconstruct pRF based on selected model."""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del train_fmri_ts
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# output directory config
roi_dir = os.path.join(prf_dir, roi)
# pRF estimate
sel_models = np.load(os.path.join(roi_dir, 'reg_sel_model.npy'))
sel_paras = np.load(os.path.join(roi_dir, 'reg_sel_paras.npy'))
sel_model_corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
prfs = np.zeros((sel_models.shape[0], 128, 128))
fig_dir = os.path.join(roi_dir, 'figs')
check_path(fig_dir)
for i in range(sel_models.shape[0]):
# get pRF
print 'Voxel %s, Val Corr %s' % (i, sel_model_corr[i])
model_idx = int(sel_models[i])
# get gaussian pooling field parameters
si = model_idx / 1024
xi = (model_idx % 1024) / 32
yi = (model_idx % 1024) % 32
x0 = np.arange(0, 128, 4)[xi]
y0 = np.arange(0, 128, 4)[yi]
s = np.linspace(1, 50, 15)[si]
#kernel = make_cycle(128, s, center=(x0, y0))
kernel = make_2d_gaussian(128, s, center=(x0, y0))
kpos = np.nonzero(kernel)
paras = sel_paras[i]
for f in range(5):
fwt = np.sum(paras[(f * 8):(f * 8 + 8)])
fs = np.sqrt(2)**f * 4
for p in range(kpos[0].shape[0]):
tmp = make_2d_gaussian(128,
fs,
center=(kpos[1][p], kpos[0][p]))
prfs[i] += fwt * kernel[kpos[0][p], kpos[1][p]] * tmp
if sel_model_corr[i] >= 0.25:
prf_file = os.path.join(fig_dir,
'Voxel_%s_%s.png' % (i + 1, vxl_idx[i]))
vutil.save_imshow(prfs[i], prf_file)
np.save(os.path.join(roi_dir, 'prfs.npy'), prfs)
def get_pls_residual(pls_dir, prf_dir, db_dir, subj_id):
pls_pred_fmri = np.load(os.path.join(pls_dir, 'pls_pred_fmri_c10.npz'))
train_pred_fmri = pls_pred_fmri['pred_train'].T
print train_pred_fmri.shape
val_pred_fmri = pls_pred_fmri['pred_val'].T
orig_fmri_data = np.load(os.path.join(prf_dir, 'roi_orig_fmri.npz'))
vxl_idx = orig_fmri_data['vxl_idx']
# ROI list
roi_list = ['v1rh', 'v1lh', 'v2rh', 'v2lh', 'v3rh', 'v3lh', 'v4rh', 'v4lh']
for roi in roi_list:
roi_idx, roi_tx, roi_vx = dataio.load_vim2_fmri(db_dir, subj_id, roi)
print roi_tx.shape
sel_idx = [i for i in range(len(vxl_idx)) if vxl_idx[i] in roi_idx]
roi_train_pred = train_pred_fmri[sel_idx]
roi_val_pred = val_pred_fmri[sel_idx]
print roi_train_pred.shape
res_train = roi_tx - roi_train_pred
res_val = roi_vx - roi_val_pred
outfile = os.path.join(prf_dir, roi, 'pls_residual_fmri')
np.savez(outfile,
pls_train_residual=res_train,
pls_val_residual=res_val,
vxl_idx=roi_idx)
def get_vxl_idx_in_rect(prf_dir, db_dir, subj_id, rmin, rmax, cmin, cmax):
"""Get voxel idx whose pRF within the specific rect."""
roi_list = ['v1rh', 'v1lh']
vxl_idx = []
rect = np.zeros((128, 128))
rect[rmin:(rmax + 1), cmin:(cmax + 1)] = 1
for roi in roi_list:
print roi
idx, tx, vx = dataio.load_vim2_fmri(db_dir, subj_id, roi)
del tx
del vx
print 'Number of voxel idx: %s' % (len(idx))
roi_dir = os.path.join(prf_dir, roi)
corr = np.load(os.path.join(roi_dir, 'reg_sel_model_corr.npy'))
prfs = np.load(os.path.join(roi_dir, 'prfs.npy'))
prfs = np.abs(prfs)
for i in range(len(idx)):
if corr[i] >= 0.25:
x = prfs[i] > 0.00005
ratio = np.sum(x * rect) / x.sum()
if ratio > 0.5:
vxl_idx.append(idx[i])
return vxl_idx
def ridge_fitting(feat_dir, prf_dir, db_dir, subj_id, roi):
"""pRF model fitting using ridge regression.
90% trainning data used for model tuning, and another 10% data used for
model seletion.
"""
# load fmri response
vxl_idx, train_fmri_ts, val_fmri_ts = dataio.load_vim2_fmri(db_dir,
subj_id,
roi=roi)
del val_fmri_ts
print 'Voxel number: %s' % (len(vxl_idx))
# load candidate models
train_models = np.load(os.path.join(feat_dir, 'train_candidate_model.npy'),
mmap_mode='r')
# output directory config
roi_dir = os.path.join(prf_dir, roi)
check_path(roi_dir)
# model seletion and tuning
ALPHA_NUM = 20
BOOTS_NUM = 15
paras_file = os.path.join(roi_dir, 'reg_paras.npy')
paras = np.memmap(paras_file,
dtype='float64',
mode='w+',
shape=(15360, len(vxl_idx), 46))
mcorr_file = os.path.join(roi_dir, 'reg_model_corr.npy')
mcorr = np.memmap(mcorr_file,
dtype='float64',
mode='w+',
shape=(15360, len(vxl_idx)))
alphas_file = os.path.join(roi_dir, 'reg_alphas.npy')
alphas = np.memmap(alphas_file,
dtype='float64',
mode='w+',
shape=(15360, len(vxl_idx)))
# fMRI data z-score
print 'fmri data temporal z-score'
m = np.mean(train_fmri_ts, axis=1, keepdims=True)
s = np.std(train_fmri_ts, axis=1, keepdims=True)
train_fmri_ts = (train_fmri_ts - m) / (1e-10 + s)
# split training dataset into model tunning set and model selection set
tune_fmri_ts = train_fmri_ts[:, :int(7200 * 0.9)]
sel_fmri_ts = train_fmri_ts[:, int(7200 * 0.9):]
# model testing
for i in range(15360):
print 'Model %s' % (i)
train_x = np.array(train_models[i, ...]).astype(np.float64)
train_x = zscore(train_x).T
# split training dataset into model tunning and selection sets
tune_x = train_x[:int(7200 * 0.9), :]
sel_x = train_x[int(7200 * 0.9):, :]
wt, r, alpha, bscores, valinds = ridge.bootstrap_ridge(
tune_x,
tune_fmri_ts.T,
sel_x,
sel_fmri_ts.T,
alphas=np.logspace(-2, 3, ALPHA_NUM),
nboots=BOOTS_NUM,
chunklen=720,
nchunks=1,
single_alpha=False,
use_corr=False)
paras[i, ...] = wt.T
mcorr[i] = r
alphas[i] = alpha
# save output
paras = np.array(paras)
np.save(paras_file, paras)
mcorr = np.array(mcorr)
np.save(mcorr_file, mcorr)
alphas = np.array(alphas)
np.save(alphas_file, alphas)