pRF Viewer
This notebook shows you how to read in the pickle-files that are generated by the line-scanning code. It shows you how to view the results on the surface using pycortex, plot specific pRFs/timecourses from vertices, and how to obtain size-response functions
[1]:
from linescanning import (
prf,
plotting,
optimal
)
import os
import matplotlib.pyplot as plt
opj = os.path.join
The files produced by the line-scanning repository will generally live in $DIR_DATA_DERIV/prf/<sub>/ses-<ses>. You can specify the specific folders below, as well as particular subject settings (e.g., subject ID, session ID, task ID, and repetition time). It will then look for the following:
BOLD data (a
npy-file ending on_hemi-LR_desc-avg_bold.npy, should live in the prf directory)Design matrix (a
mat-file calleddesign_task-<taskID>, should live in the prf directory)Model files (
pkl-files containingmodel-flags in the filename)
[6]:
# define project directory
# proj_dir = "/data1/projects/MicroFunc/Zoey/projects"
# proj_name = "pilot1"
proj_dir = "/data1/projects/MicroFunc/Jurjen/projects"
proj_name = "VE-SRF"
deriv = opj(proj_dir, proj_name, "derivatives")
# define subject settings
sub = "005"
ses = "1"
task = "2R"
TR = 1.5
# find BOLD data
prf_dir = opj(deriv, "prf", f"sub-{sub}", f"ses-{ses}")
bold_file = opj(prf_dir, f"sub-{sub}_ses-{ses}_task-{task}_hemi-LR_desc-avg_bold.npy")
print(f"BOLD:\t{bold_file}")
dm_file = opj(prf_dir, f"design_task-{task}.mat")
print(f"Design:\t{dm_file}")
# find model files
model_files = {}
for model in ["gauss","norm","css","dog"]:
pkl_file = opj(prf_dir, f"sub-{sub}_ses-{ses}_task-{task}_model-{model}_stage-iter_desc-prf_params.pkl")
if os.path.exists(pkl_file):
model_files[model] = pkl_file
for key,val in model_files.items():
print(f"{key}:\t{val}")
BOLD: /data1/projects/MicroFunc/Jurjen/projects/VE-SRF/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_hemi-LR_desc-avg_bold.npy
Design: /data1/projects/MicroFunc/Jurjen/projects/VE-SRF/derivatives/prf/sub-005/ses-1/design_task-2R.mat
gauss: /data1/projects/MicroFunc/Jurjen/projects/VE-SRF/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_model-gauss_stage-iter_desc-prf_params.pkl
norm: /data1/projects/MicroFunc/Jurjen/projects/VE-SRF/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_model-norm_stage-iter_desc-prf_params.pkl
[5]:
!call_ctxfilestore show_fs
/data1/projects/MicroFunc/Jurjen/projects/VE-SRF/derivatives/pycortex
Using linescanning.optimal.pRFCalc, we can quickly parse the pRF-estimates into a dataframe given the model-type (e.g., norm). This class then also created pycortex objects than can be opened by calling .open_pycortex(). For some reason, this seems to work better if your default browser is Chrome. The function will spit out colorbars for the different elements (r2, eccentricity, and polar angle), as well as the vertex ID with the highest variance explained.
[26]:
%matplotlib inline
check_model = "norm"
# plot parameters on surface
skip_ctx = False
prf_obj = optimal.pRFCalc(model_files[check_model], skip_cortex=skip_ctx)
if not skip_ctx:
prf_obj.open_pycortex(
fig_dir="/data1/projects/MicroFunc/Jurjen/projects/VE-SRF/derivatives/pycortex/sub-005/cmap_test",
base_name="sub-005_cmap-uint"
)
print(f"max r2 = {round(prf_obj.max_r2,2)} | vert = {prf_obj.max_r2_vert}")
Started server on port 24030
max r2 = 0.91 | vert = 313900
[27]:
prf_obj.pyc.save_all(gallery=True)
saving r2
saving ecc
saving polar
saving B
saving D
saving ratio_bd
saving /data1/projects/MicroFunc/Jurjen/projects/VE-SRF/derivatives/pycortex/sub-005/cmap_test/sub-005_cmap-uint_desc-brainmaps.pdf
Stopping server
[82]:
# load_params function can deal with this type of dictionary input
model_files
[82]:
{'gauss': '/data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_model-gauss_stage-iter_desc-prf_params.pkl',
'norm': '/data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_model-norm_stage-iter_desc-prf_params.pkl'}
We can then load in the data/models using the linescanning.prf.pRFmodelFitting class (see also the pRFmodelFItting-notebook). This class accepts the dictionary-like input printed above, and loads them in as <model>_iter, which stands for the iterative search parameters of a specified model. This we can then use when calling the plot_vox() function below.
[83]:
# initiate object
obj = prf.pRFmodelFitting(
bold_file,
design_matrix=dm_file,
TR=TR,
model=check_model,
verbose=True,
)
# load parameters
obj.load_params(
model_files,
stage="iter",
model=None
)
Reading design matrix from '/data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1/design_task-2R.mat'
Reading data from '/data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_hemi-LR_desc-avg_bold.npy'
Skipped volumes was negative (-266216), transposing data to (266441, 221)
Design has 4 more volumes than timecourses, trimming from beginning of design to (54, 54, 221)
Reading settings from '/data1/projects/MicroFunc/Jurjen/programs/packages/linescanning/misc/prf_analysis.yml'
---------------------------------------------------------------------------------------------------
Check these important settings!
Screen distance: 196cm
Screen size: 39.3cm
TR: 1.5s
---------------------------------------------------------------------------------------------------
Instantiate HRF with: [1, 4.6, 0] (fit=True)
Using constraint(s): ['tc', 'tc']
Reading settings from '/data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_model-gauss_stage-iter_desc-prf_params.pkl' (safest option; overwrites other settings)
---------------------------------------------------------------------------------------------------
Check these important updated settings!
Screen distance: 196cm
Screen size: 39.3cm
TR: 1.5s
---------------------------------------------------------------------------------------------------
Inserting parameters from <class 'str'> as 'gauss_iter' in <linescanning.prf.pRFmodelFitting object at 0x7f89d917b1c0>
Reading settings from '/data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_model-norm_stage-iter_desc-prf_params.pkl' (safest option; overwrites other settings)
---------------------------------------------------------------------------------------------------
Check these important updated settings!
Screen distance: 196cm
Screen size: 39.3cm
TR: 1.5s
---------------------------------------------------------------------------------------------------
Inserting parameters from <class 'str'> as 'norm_iter' in <linescanning.prf.pRFmodelFitting object at 0x7f89d917b1c0>
Here we can choose to plot the pRF and the timecourse (data+prediction) of a given vertex, with the model of our choosing. Here we choose norm, which represents the divisive-normalization model. If you have other models in the model_files-dictionary, you can specify those here to see how the prediction changes based on selected model
[85]:
%matplotlib inline
plot_vert = prf_obj.max_r2_vert
_ = obj.plot_vox(vox_nr=plot_vert, model="norm", title="pars")
The DN-model allows for modeling of the response of pRFs given a certain stimulus size, as it’s able to capture both non-linearities as the beginning of the curve and at the end. You can submit a job that creates SRFs for all vertices in the brain based on the DN-model parameters
[86]:
# define command
split_file = os.path.basename(model_files["norm"]).split("_")
desc_idx = split_file.index("desc-prf")
base_name = "_".join(split_file[:desc_idx])+"_desc-srfs_centered"
cmd = f"qsub -N {base_name} -wd {os.path.dirname(model_files['norm'])} -q long.q {opj(os.environ.get('DIR_SCRIPTS'), 'bin', 'call_sizeresponse')} --in {model_files['norm']} --verbose"
print(cmd)
qsub -N sub-005_ses-1_task-2R_model-norm_stage-iter_desc-srfs_centered -wd /data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1 -q long.q /data1/projects/MicroFunc/Jurjen/programs/packages/linescanning/bin/call_sizeresponse --in /data1/projects/MicroFunc/Zoey/projects/pilot1/derivatives/prf/sub-005/ses-1/sub-005_ses-1_task-2R_model-norm_stage-iter_desc-prf_params.pkl --verbose
[87]:
# run command
os.system(cmd)
Your job 32732 ("sub-005_ses-1_task-2R_model-norm_stage-iter_desc-srfs_centered") has been submitted
[87]:
0
Or you can run the process for a single vertex
[88]:
fig,axs = plt.subplots(figsize=(5,5))
# plot the model fit
pars,_,tc,pred = obj.plot_vox(
vox_nr=plot_vert,
make_figure=False,
model="norm"
)
# calculate sizeresponse
SR_ = prf.SizeResponse(params=pars, model="norm")
## CENTERED PRF
# size response
fill_cent, fill_cent_sizes = SR_.make_stimuli(
factor=1,
dt="fill"
)
sr_cent_act = SR_.batch_sr_function(
SR_.params_df,
center_prf=True,
stims=fill_cent,
sizes=fill_cent_sizes
)
# hole-response
hole_cent, hole_cent_sizes = SR_.make_stimuli(
factor=1,
dt="hole"
)
sr_cent_norm = SR_.batch_sr_function(
SR_.params_df,
center_prf=True,
stims=hole_cent,
sizes=hole_cent_sizes
)
%matplotlib inline
## PLOT
plotting.LazyPlot(
[df.iloc[:,0].values for df in [sr_cent_act,sr_cent_norm]],
xx=fill_cent_sizes,
color=["#1B9E77","#D95F02"],
line_width=3,
axs=axs,
x_label="stimulus size",
y_label="response",
labels=["act","suppr"],
add_hline=0,
title=f"vox-{plot_vert}",
x_lim=[0,5]
)
max_dva, max_val = SR_.find_stim_sizes(
sr_cent_act[0].values,
t="max",
dt="fill",
sizes=fill_cent_sizes,
return_ampl=True
)
print(f" Max stimulation @{round(max_dva,2)}dva | ampl = {round(max_val,2)}")
min_dva, min_val = SR_.find_stim_sizes(
sr_cent_norm[0].values,
t="min",
dt="fill",
sizes=fill_cent_sizes,
return_ampl=True
)
print(f" Min stimulation @{round(min_dva,2)}dva | ampl = {round(min_val,2)}")
Max stimulation @1.64dva | ampl = 14.77
Min stimulation @4.91dva | ampl = -7.59
[78]:
# plot stimuli
prf.plot_stims(fill_cent, extent=SR_.vf_extent, interval=2)
prf.plot_stims(hole_cent, extent=SR_.vf_extent, interval=2)
