Revert "Merge with Julian's updated branch"

This reverts commit 09f608c.

Author: jkosciessa

.gitignore

@@ -80,4 +80,4 @@ $RECYCLE.BIN/
 .directory
 .Trash-*
 core.*
-.Rhistory
+

.gitmodules

@@ -24,30 +24,9 @@ cp /opt/prestus/example_data/PRESTUS_example_data.zip ${HOME}
 
 Download and install these tools:
 
-- MATLAB (R2022b)
-- [SimNIBS 4](https://github.com/simnibs/simnibs)
-- toolboxes included as submodules if this repository is cloned (must be added on MATLAB startup)
-    - [k-Wave (1.4)](https://github.com/ucl-bug/k-wave.git)
-    - [export_fig](https://github.com/altmany/export_fig)
-    - [FEX-minimize](https://github.com/rodyo/FEX-minimize.git)
-    - [xml2struct](https://github.com/joe-of-all-trades/xml2struct)
-
-Tested on MATLAB 2022b, set up to work on Donders HPC (can work on a local PC as well). 
-
-Before using the package, you need to have some libraries on your path. Major dependencies are included as submodules in the toolbox folder. If you clone this repository, you can retrieve the submodules as follows:
-```
-git clone --recurse-submodules https://github.com/Donders-Institute/PRESTUS.git
-```
-
-If you cloned this repository in the past, and updated it, you can retrieve submodules as follows:
-```
-cd PRESTUS
-git submodule init
-git submodule update
-```
-You additionally need to install SimNIBS (https://simnibs.github.io/simnibs/build/html/index.html#simnibs-4).
-
-*Note: If you do not clone this repository, you must manually download and add the toolboxes specified above.*
+- [SimNIBS 4](https://simnibs.github.io/simnibs/build/html/index.html#simnibs-4)
+- [k-Wave 1.4](http://www.k-wave.org/download.php) (should be installed in the 'toolbox' folder of PRESTUS or be added automatically on MATLAB startup if you use HPC)
+- toolboxes included in this repository
 
 Example data: We are currently working on a solution to make the example dataset available for users outside the DCCN.
 

README.md

@@ -0,0 +1,38 @@
+transducer: 
+  n_elements: 2 # number of elements in the transducer
+  Elements_ID_mm: [0, 32.6644] # elements 1 & 2 inner diameter [mm]
+  Elements_OD_mm: [32.1564, 45.4914] # element 1 & 2 outer diameter [mm]
+  curv_radius_mm: 63.20 # radius from the focal point to the bowl outermost point
+  dist_to_plane_mm: 56.87 # distance to the transducer plane from the geometric focus
+  source_amp: 126e3 # [Pa] (calibrated values at 20 W/cm^2 free-water Isppa)
+  source_phase_rad: [0,2.0381] # [rad] (calibrated values at 20 W/cm^2 free-water Isppa)
+  source_freq_hz: 250e3  # [Hz]
+
+
+expected_focal_distance_mm: 28.0 # expected distance to the stimulation focus
+transducer_from_localite: 1 # transducer position is to be taken from the localite file
+
+# distance from the reference used in the neuronavigation (could be the TMS coil or the three-ball reference) and the transducer
+reference_transducer_distance_mm: 18
+
+data_path: /project/2422024.01/M1TUS_2
+
+t1_path_template: P%1$02d/*_T1w.nii.gz # path to T1 relative to data_path; all string substitutions will be done using subject_id
+t2_path_template: P%1$02d/*_T2w.nii.gz # path to T2 relative to data_path; all string substitutions will be done using subject_id
+localite_instr_file_template: P%1$02d/Instrument*.xml  # path to the localite file that has the data about the instrument relative to data_path; could also be a template similar to t1 and t2 path (usually an xml file taken from subject/Sessions/Session_xxxx/InstrumentMarkers/ folder)
+
+run_heating_sims: 1
+
+default_grid_dims: [144, 144, 256]
+
+thermal:
+  duty_cycle: 0.3 # share of the stimulation duration during which the stimulation is on
+  on_off_step_duration: 0.1 # duration of the on+off cycle (e.g., with a duty cycle of 0.3 and 0.01 s time steps for simulation, the whole on+off cycle will take 0.1 s)
+  equal_steps: 0 # is the duration of the simulation steps equal for on and off steps? if not, it is computed based on the sim_time_steps * n_steps where n_steps is the needed number of on and off steps derived from the duty cycle
+  temp_0: 37 #[deg C] initial temperature, currently not used
+  stim_duration: 0.5 # [s] stimulation duration within a trial
+  iti: 5 # interval between the trials, from the start of one trial to the start of another [s]
+  n_trials: 2 # number of trials to simulate; the total simulated duration is then n_trials*iti seconds
+  sensor_xy_halfsize: 100 # maximum size of the sensor window in which the temperature is recorded (in grid units)
+  sim_time_steps: 0.01 # [s] simulation time steps during the stimulation period
+  post_stim_time_step_dur: 0.1 # post-stimulation (inter-trial) steps

configs/M1_project_config.yaml

@@ -0,0 +1,36 @@
+transducer: 
+  n_elements: 2 # number of elements in the transducer
+  Elements_ID_mm: [0, 32.6644] # elements 1 & 2 inner diameter [mm]
+  Elements_OD_mm: [32.1564, 45.4914] # element 1 & 2 outer diameter [mm]
+  curv_radius_mm: 63.20 # radius from the focal point to the bowl outermost point
+  dist_to_plane_mm: 56.87 # distance to the transducer plane from the geometric focus
+  source_amp: 122277 # [Pa] (calibrated values at 20 W/cm^2 free-water Isppa)
+  source_phase_rad: [0, 2.0381] # [rad] (calibrated values at 20 W/cm^2 free-water Isppa)
+  source_freq_hz: 250e3  # [Hz]
+
+
+expected_focal_distance_mm: 28.0 # expected distance to the stimulation focus
+transducer_from_localite: 1 # transducer position is to be taken from the localite file
+
+# distance from the reference used in the neuronavigation (could be the TMS coil or the three-ball reference) and the transducer
+reference_transducer_distance_mm: 18
+
+data_path: /project/2422024.01/M1TUS_2
+
+t1_path_template: P%1$02d/*_T1w.nii.gz # path to T1 relative to data_path; all string substitutions will be done using subject_id
+t2_path_template: P%1$02d/*_T2w.nii.gz # path to T2 relative to data_path; all string substitutions will be done using subject_id
+localite_instr_file_template: P%1$02d/Instrument*.xml  # path to the localite file that has the data about the instrument relative to data_path; could also be a template similar to t1 and t2 path (usually an xml file taken from subject/Sessions/Session_xxxx/InstrumentMarkers/ folder)
+
+run_heating_sims: 1
+
+default_grid_dims: [144, 144, 256]
+
+thermal:
+  duty_cycle: 0.3 # share of the stimulation duration during which the stimulation is on
+  on_off_step_duration: 0.1 # duration of the on+off cycle (e.g., with a duty cycle of 0.3 and 0.01 s time steps for simulation, the whole on+off cycle will take 0.1 s)
+  equal_steps: 0 # is the duration of the simulation steps equal for on and off steps? if not, it is computed based on the sim_time_steps * n_steps where n_steps is the needed number of on and off steps derived from the duty cycle
+  sim_time_steps: 0.01 # [s] simulation time steps during the stimulation period
+  post_stim_time_step_dur: 0.1 # post-stimulation (inter-trial) steps
+  stim_duration: 0.5 # [s] stimulation duration within a trial
+  iti: 5 # interval between the trials, from the start of one trial to the start of another [s]
+  n_trials: 2 # number of trials to simulate; the total simulated duration is then n_trials*iti seconds

configs/M1_project_config_opt_21W.yaml

@@ -0,0 +1,46 @@
+# Location of stored data
+data_path: /project/3023001.06/Simulations/data_for_prestus/
+simnibs_bin_path: /home/mrphys/kenvdzee/SimNIBS-4.0/bin/
+subject_subfolder: 1
+output_location: /project/ change to ben's project
+
+overwrite_simnibs: 0
+
+# Structure of subfolders containing T1 and T1 images
+## It is easier to store the subject data of each participant in an individual subfolder
+t1_path_template: sub-%1$03d/*t1mprage*T1w.nii.gz
+t2_path_template: sub-%1$03d/*t2space*T2w.nii.gz
+
+transducer: 
+  n_elements: 4 # number of elements in the transducer
+  Elements_ID_mm: [0, 30.1788, 42.1388, 51.1088]
+  Elements_OD_mm: [29.62, 41.58, 50.55, 57.94]
+  curv_radius_mm: 62.94 # radius of curvature of the bowl 
+  dist_to_plane_mm: 52.38 # distance to the transducer plane from the geometric focus
+  source_amp: 199270 # [Pa]
+  source_phase_deg: [0, 300.544203, 308.222241, 283.413768] # source phase [deg]
+  source_freq_hz: 250e3 # [Hz] the central frequency
+  pos_t1_grid: [number, number, number]
+
+focus_pos_t1_grid: [number, number, number]
+
+expected_focal_distance_mm: 60.9 # expected distance to the stimulation focus
+transducer_from_localite: 0 # should we load the transducer locations from the localite file(s) 
+
+using_donders_hpc: 1 # are the simulations run on the HPC cluster?
+
+run_posthoc_water_sims: 0
+run_heating_sims: 0
+
+thermal:
+  duty_cycle: 0.3 # share of the stimulation duration during which the stimulation is on [0 to 1] (trial length = duty_cycle * stim_duration)
+  iti: 14 # [s] interval between the trials, from the start of one trial to the start of another
+  n_trials: 60 # number of trials to simulate; the total simulated duration is then n_trials*iti seconds
+  stim_duration: 1 # [s] stimulation duration within a trial
+  # Pulse repetition frequency is not used since the cooling effects between these cycles are limited
+
+  # These should only be changed if they don't meet the criteria described in "run_heating_simulations"
+  sim_time_steps: 0.01 # [s] simulation time steps during the stimulation period
+  post_stim_time_step_dur: 0.1 # post-stimulation (inter-trial) steps
+  on_off_step_duration: 0.1 # duration of the on+off cycle (e.g., with a duty cycle of 0.3 and 0.01 s time steps for simulation, the whole on+off cycle will take 0.1 s)
+  equal_steps: 0 # is the duration of the simulation steps equal for on and off steps? if not, it is computed based on the sim_time_steps * n_steps where n_steps is the needed number of on and off steps derived from the duty cycle

configs/ben_unnamed_project_CTX250-001_203_60.9mm.yaml

@@ -0,0 +1,24 @@
+data_path: /home/visual/andche/STAFF_SCI/andche_sandbox/Sjoerd_MRI/
+t1_path_template: MRI/sub-%1$03d/ses-mri01/anat/*T1w.nii.gz
+t2_path_template: MRI/sub-%1$03d/ses-mri01/anat/*T2w.nii.gz
+
+transducer: 
+  n_elements: 4 # number of elements in the transducer
+  Elements_ID_mm: [0, 32.9184, 46.1264, 56.0324]
+  Elements_OD_mm: [32.3596, 45.5676, 55.5244, 64.008]
+  curv_radius_mm: 63.20 # radius of curvature of the bowl 
+  dist_to_plane_mm: 52.38 # distance to the transducer plane from the geometric focus
+  source_amp: 145103 # [Pa] (calibrated values at 20 W/cm^2 free-water Isppa)
+  source_phase_deg: [0, 0, 358.0546, 272.2390] # source phase [deg] (calibrated values at 20 W/cm^2 free-water Isppa)
+  source_freq_hz: 250e3 # [Hz] the central frequency
+
+transducer_from_localite: 0 # should we load the transducer locations from the localite file(s) 
+thermal:
+  duty_cycle: 0.3 # share of the stimulation duration during which the stimulation is on
+  on_off_step_duration: 0.1 # duration of the on+off cycle (e.g., with a duty cycle of 0.3 and 0.01 s time steps for simulation, the whole on+off cycle will take 0.1 s)
+  equal_steps: 0 # is the duration of the simulation steps equal for on and off steps? if not, it is computed based on the sim_time_steps * n_steps where n_steps is the needed number of on and off steps derived from the duty cycle
+  sim_time_steps: 0.01 # [s] simulation time steps during the stimulation period
+  post_stim_time_step_dur: 0.1 # post-stimulation (inter-trial) steps
+  stim_duration: 3 # [s] stimulation duration within a trial
+  iti: 9 # interval between the trials, from the start of one trial to the start of another [s]
+  n_trials: 4 # number of trials to simulate; the total simulated duration is then n_trials*iti seconds

configs/bob_config_opt_CTX250-001_64.5mm.yaml

@@ -0,0 +1,25 @@
+data_path: /home/visual/andche/STAFF_SCI/andche_sandbox/Sjoerd_MRI/
+t1_path_template: MRI/sub-%1$03d/ses-mri01/anat/*T1w.nii.gz
+t2_path_template: MRI/sub-%1$03d/ses-mri01/anat/*T2w.nii.gz
+
+transducer: 
+  n_elements: 4 # number of elements in the transducer
+  Elements_ID_mm: [0, 32.9184, 46.1264, 56.0324]
+  Elements_OD_mm: [32.3596, 45.5676, 55.5244, 64.008]
+  curv_radius_mm: 63.20 # radius of curvature of the bowl 
+  dist_to_plane_mm: 52.38 # distance to the transducer plane from the geometric focus
+  source_amp: 143805 # [Pa] (calibrated values at 30 W/cm^2 free-water Isppa)
+  source_phase_deg: [0, 0, 332.8122, 264.4677] # source phase [deg] (calibrated values at 30 W/cm^2 free-water Isppa)
+  source_freq_hz: 250e3 # [Hz] the central frequency
+
+transducer_from_localite: 0 # should we load the transducer locations from the localite file(s) 
+
+thermal:
+  duty_cycle: 0.3 # share of the stimulation duration during which the stimulation is on
+  on_off_step_duration: 0.1 # duration of the on+off cycle (e.g., with a duty cycle of 0.3 and 0.01 s time steps for simulation, the whole on+off cycle will take 0.1 s)
+  equal_steps: 0 # is the duration of the simulation steps equal for on and off steps? if not, it is computed based on the sim_time_steps * n_steps where n_steps is the needed number of on and off steps derived from the duty cycle
+  sim_time_steps: 0.01 # [s] simulation time steps during the stimulation period
+  post_stim_time_step_dur: 0.1 # post-stimulation (inter-trial) steps
+  stim_duration: 3 # [s] stimulation duration within a trial
+  iti: 9 # interval between the trials, from the start of one trial to the start of another [s]
+  n_trials: 4 # number of trials to simulate; the total simulated duration is then n_trials*iti seconds

configs/bob_config_opt_CTX250-011_64.5mm.yaml

@@ -0,0 +1,34 @@
+subject_subfolder: 1 # Should each participants output be stored in a separate folder?
+
+t1_path_template: /*T1.nii.gz
+t2_path_template: /*T2.nii.gz
+
+transducer: 
+  n_elements: 4 # number of elements in the transducer
+  Elements_ID_mm: [0, 32.9184, 46.1264, 56.0324]
+  Elements_OD_mm: [32.3596, 45.5676, 55.5244, 64.008]
+  curv_radius_mm: 63.20 # radius of curvature of the bowl 
+  dist_to_plane_mm: 52.38 # distance to the transducer plane from the geometric focus
+  source_amp: 143000 # [Pa] (143000 calibrated values at 30 W/cm^2 free-water Isppa, 166500 at 40 W/cm^2, 184200 for 50 W/cm^2)
+  source_phase_deg: [0, 0, 358.0546, 272.2390] # source phase [deg] (calibrated values at 20 W/cm^2 free-water Isppa)
+  source_freq_hz: 250e3 # [Hz] the central frequency
+
+expected_focal_distance_mm: 64.5 # expected distance to the stimulation focus
+transducer_from_localite: 0 # should we load the transducer locations from the localite file(s)
+
+using_donders_hpc: 1 # are the simulations run on the HPC cluster?
+
+run_posthoc_water_sims: 1
+run_heating_sims: 1
+
+medium:
+  skull:
+    alpha_0_true: 8
+
+thermal:
+  duty_cycle: 0.5 # share of the stimulation duration during which the stimulation is on
+  sim_time_steps: 0.1 # [s] simulation time steps during the stimulation period
+  temp_0: 37 #[deg C] initial temperature, currently not used
+  stim_duration: 120 # [s] stimulation duration within a trial
+  iti: 0 # interval between the trials, from the start of one trial to the start of another [s]
+  n_trials: 1 # number of trials to simulate; the total simulated duration is then n_trials*iti seconds