From 745353a49d78b283c99f19c0312598feb93a0eed Mon Sep 17 00:00:00 2001
From: matsvanes <mats.vanes@psych.ox.ac.uk>
Date: Fri, 19 Jan 2024 14:33:36 +0000
Subject: [PATCH 01/11] save extra_funcs from preproc chain to
 raw.info['description'] and display in summary report

---
 osl/preprocessing/batch.py                  | 11 +++++--
 osl/report/preproc_report.py                | 36 +++++++++++++++++++++
 osl/report/templates/raw_summary_panel.html |  1 +
 3 files changed, 46 insertions(+), 2 deletions(-)

diff --git a/osl/preprocessing/batch.py b/osl/preprocessing/batch.py
index e51d1498..7ff94075 100644
--- a/osl/preprocessing/batch.py
+++ b/osl/preprocessing/batch.py
@@ -22,6 +22,7 @@
 from functools import partial, wraps
 from time import localtime, strftime
 from datetime import datetime
+import inspect
 
 import mne
 import numpy as np
@@ -299,7 +300,7 @@ def get_config_from_fif(inst):
     return config
 
 
-def append_preproc_info(dataset, config):
+def append_preproc_info(dataset, config, extra_funcs=None):
     """Add to the config of already preprocessed data to ``inst.info['description']``.
 
     Parameters
@@ -325,6 +326,12 @@ def append_preproc_info(dataset, config):
         + f"VERSION: {__version__}\n"
         + f"%% config start %% \n{config} \n%% config end %%"
     )
+    
+    if extra_funcs is not None:
+        preproc_info += "\n\nCUSTOM FUNCTIONS USED:\n"
+        for func in extra_funcs:
+            preproc_info += f"%% extra_funcs start %% \n{inspect.getsource(func)}\n%% extra_funcs end %%"
+    
     dataset["raw"].info["description"] = (
         dataset["raw"].info["description"] + preproc_info
     )
@@ -745,7 +752,7 @@ def run_proc_chain(
             dataset = func(dataset, userargs)
 
         # Add preprocessing info to dataset dict
-        dataset = append_preproc_info(dataset, config)
+        dataset = append_preproc_info(dataset, config, extra_funcs)
 
         fif_outname = None
         if outdir is not None:
diff --git a/osl/report/preproc_report.py b/osl/report/preproc_report.py
index 6926017e..0a44d9de 100644
--- a/osl/report/preproc_report.py
+++ b/osl/report/preproc_report.py
@@ -15,6 +15,7 @@
 import tempfile
 import pickle
 import pathlib
+import re
 
 import numpy as np
 import matplotlib.pyplot as plt
@@ -192,6 +193,7 @@ def gen_html_data(raw, outdir, ica=None, preproc_fif_filename=None):
     
     # Generate plots for the report
     data["plt_config"] = plot_flowchart(raw, savebase)
+    data["txt_extra_funcs"] = save_extra_funcs(raw, savebase.replace('.png', '.txt'))
     data['plt_temporalsumsq'] = plot_channel_time_series(raw, savebase, exclude_bads=False)
     data['plt_temporalsumsq_exclude_bads'] = plot_channel_time_series(raw, savebase, exclude_bads=True)
     data['plt_badchans'] = plot_sensors(raw, savebase)
@@ -317,6 +319,7 @@ def gen_html_summary(reportdir):
     os.makedirs(f"{reportdir}/summary", exist_ok=True)
 
     data["plt_config"] = subject_data[0]["plt_config"]
+    data["txt_extra_funcs"] = subject_data[0]["txt_extra_funcs"]
     data["plt_summary_bad_segs"] = plot_summary_bad_segs(subject_data, reportdir)
     data["plt_summary_bad_chans"] = plot_summary_bad_chans(subject_data, reportdir)
 
@@ -419,6 +422,39 @@ def plot_flowchart(raw, savebase=None):
         fpath = None
     return fpath
 
+
+def save_extra_funcs(raw, savebase=None):
+    """ Saves extra functions from the raw.info['description'] to a text file.
+    
+    Parameters
+    ----------
+    raw : :py:class:`mne.io.Raw <mne.io.Raw>`
+        MNE Raw object.
+    savebase : str
+        Base string for saving figures.
+        
+    Returns
+    -------
+    fpath : str
+        Path to saved text file.
+    
+    """
+    extra_funcs = re.findall(
+    "%% extra_funcs start %%(.*?)%% extra_funcs end %%",
+    raw.info["description"],
+    flags=re.DOTALL,
+    )
+    
+    if savebase is not None:
+        fpath = savebase.format(f"extra_funcs")
+        with(open(fpath, 'w')) as file:
+            [print(func, file=file) for func in extra_funcs]
+        return fpath
+    else:
+        return None
+    
+        
+
 def plot_channel_time_series(raw, savebase=None, exclude_bads=False):
     """Plots sum-square time courses.
     
diff --git a/osl/report/templates/raw_summary_panel.html b/osl/report/templates/raw_summary_panel.html
index 67f33dd2..8b651edb 100644
--- a/osl/report/templates/raw_summary_panel.html
+++ b/osl/report/templates/raw_summary_panel.html
@@ -14,6 +14,7 @@
     <div class="tabpage" style='width: 100%' id='config'>
         <h3>Config</h3>
         <img src="{{ data.plt_config }}" alt="" style='max-width: 60%'/>
+        <iframe src="{{ data.txt_extra_funcs }}" style="width: 80%; height: 200px;"></iframe>
     </div>
 
     <div class="tabpage" style='width: 100%' id='time'>

From 682e44c940dd7321b588b888d046ecf39ea522c1 Mon Sep 17 00:00:00 2001
From: matsvanes <mats.vanes@psych.ox.ac.uk>
Date: Fri, 19 Jan 2024 19:24:24 +0000
Subject: [PATCH 02/11] add title

---
 osl/report/templates/raw_summary_panel.html | 1 +
 1 file changed, 1 insertion(+)

diff --git a/osl/report/templates/raw_summary_panel.html b/osl/report/templates/raw_summary_panel.html
index 8b651edb..15096372 100644
--- a/osl/report/templates/raw_summary_panel.html
+++ b/osl/report/templates/raw_summary_panel.html
@@ -14,6 +14,7 @@
     <div class="tabpage" style='width: 100%' id='config'>
         <h3>Config</h3>
         <img src="{{ data.plt_config }}" alt="" style='max-width: 60%'/>
+        <h3>Extra functions</h3>
         <iframe src="{{ data.txt_extra_funcs }}" style="width: 80%; height: 200px;"></iframe>
     </div>
 

From 483810a75df53247daf9e6b88d955bb3807e0ac6 Mon Sep 17 00:00:00 2001
From: matsvanes <mats.vanes@psych.ox.ac.uk>
Date: Sat, 20 Jan 2024 11:07:52 +0000
Subject: [PATCH 03/11] add extra_funcs to source report

---
 osl/report/src_report.py                    | 34 ++++++++++++++++++++-
 osl/report/templates/src_summary_panel.html |  2 ++
 osl/source_recon/batch.py                   |  2 +-
 3 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/osl/report/src_report.py b/osl/report/src_report.py
index 03e5ca68..cf43a1c4 100644
--- a/osl/report/src_report.py
+++ b/osl/report/src_report.py
@@ -3,6 +3,7 @@
 """
 
 # Authors: Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
+# Mats van Es <mats.vanes@psych.ox.ac.uk>
 
 import os
 import os.path as op
@@ -13,12 +14,13 @@
 import numpy as np
 import matplotlib.pyplot as plt
 from tabulate import tabulate
+import inspect
 
 from . import preproc_report
 from ..source_recon import parcellation
 
 
-def gen_html_data(config, src_dir, subject, reportdir, logger=None):
+def gen_html_data(config, src_dir, subject, reportdir, logger=None, extra_funcs=None):
     """Generate data for HTML report.
 
     Parameters
@@ -33,6 +35,8 @@ def gen_html_data(config, src_dir, subject, reportdir, logger=None):
         Report directory.
     logger : logging.getLogger
         Logger.
+    extra_funcs : list
+        List of extra functions to run
     """
     src_dir = Path(src_dir)
     reportdir = Path(reportdir)
@@ -63,6 +67,8 @@ def gen_html_data(config, src_dir, subject, reportdir, logger=None):
         data = {}
         data["config"] = config
 
+    data['extra_funcs'] = save_extra_funcs(extra_funcs, reportdir / subject)
+    
     data["fif_id"] = subject
     data["filename"] = subject
 
@@ -116,6 +122,31 @@ def gen_html_data(config, src_dir, subject, reportdir, logger=None):
     pickle.dump(data, open(f"{reportdir}/{subject}/data.pkl", "wb"))
 
 
+def save_extra_funcs(extra_funcs, reportdir):
+    """ Saves extra functions to a text file.
+    
+    Parameters
+    ----------
+    extra_funcs : list
+        List of extra functions to save.
+    reportdir : str
+        Subject report directory.
+        
+    Returns
+    -------
+    fpath : str
+        Path to saved text file.
+    """
+    
+    if reportdir is not None:
+        fpath = reportdir / 'extra_funcs.txt'
+        with(open(fpath, 'w')) as file:
+            [print(f"{inspect.getsource(func)}\n\n", file=file) for func in extra_funcs]
+        return fpath
+    else:
+        return None
+
+
 def gen_html_page(reportdir):
     """Generate an HTML page from a report directory.
 
@@ -215,6 +246,7 @@ def gen_html_summary(reportdir):
     data = {}
     data["total"] = total
     data["config"] = subject_data[0]["config"]
+    data["extra_funcs"] = subject_data[0]["extra_funcs"]
     data["coregister"] = subject_data[0]["coregister"]
     data["beamform"] = subject_data[0]["beamform"]
     data["beamform_and_parcellate"] = subject_data[0]["beamform_and_parcellate"]
diff --git a/osl/report/templates/src_summary_panel.html b/osl/report/templates/src_summary_panel.html
index f12cadc8..270b4575 100644
--- a/osl/report/templates/src_summary_panel.html
+++ b/osl/report/templates/src_summary_panel.html
@@ -21,6 +21,8 @@
     <div class="tabpage" style='width: 100%' id='config'>
         <h3>Config</h3>
         <img src="{{ data.plt_config }}" alt="" style='max-width: 60%'/>
+        <h3>Extra functions</h3>
+        <iframe src="{{ data.extra_funcs }}" style="width: 80%; height: 200px;"></iframe>
     </div>
 
     {% if data.coregister %}
diff --git a/osl/source_recon/batch.py b/osl/source_recon/batch.py
index 5b7d4668..ff36eee6 100644
--- a/osl/source_recon/batch.py
+++ b/osl/source_recon/batch.py
@@ -204,7 +204,7 @@ def run_src_chain(
         return False
 
     # Generate HTML data for the report
-    src_report.gen_html_data(config, src_dir, subject, reportdir)
+    src_report.gen_html_data(config, src_dir, subject, reportdir, extra_funcs=extra_funcs)
 
     return True
 

From a61027bfaee5f6298397a814a9331fe6e7c03eff Mon Sep 17 00:00:00 2001
From: matsvanes <mats.vanes@psych.ox.ac.uk>
Date: Sat, 20 Jan 2024 11:38:28 +0000
Subject: [PATCH 04/11] add raw data plot to time series panel

---
 osl/report/preproc_report.py                | 34 +++++++++++++++++++++
 osl/report/templates/raw_subject_panel.html |  4 +++
 2 files changed, 38 insertions(+)

diff --git a/osl/report/preproc_report.py b/osl/report/preproc_report.py
index 0a44d9de..29f64ae6 100644
--- a/osl/report/preproc_report.py
+++ b/osl/report/preproc_report.py
@@ -194,6 +194,7 @@ def gen_html_data(raw, outdir, ica=None, preproc_fif_filename=None):
     # Generate plots for the report
     data["plt_config"] = plot_flowchart(raw, savebase)
     data["txt_extra_funcs"] = save_extra_funcs(raw, savebase.replace('.png', '.txt'))
+    data["plt_rawdata"] = plot_rawdata(raw, savebase)
     data['plt_temporalsumsq'] = plot_channel_time_series(raw, savebase, exclude_bads=False)
     data['plt_temporalsumsq_exclude_bads'] = plot_channel_time_series(raw, savebase, exclude_bads=True)
     data['plt_badchans'] = plot_sensors(raw, savebase)
@@ -455,6 +456,39 @@ def save_extra_funcs(raw, savebase=None):
     
         
 
+def plot_rawdata(raw, savebase):
+    """Plots raw data.
+    
+    Parameters
+    ----------
+    raw : :py:class:`mne.io.Raw <mne.io.Raw>`
+        MNE Raw object.
+    savebase : str
+        Base string for saving figures.
+        
+    Returns
+    -------
+    fpath : str
+        Path to saved figure.      
+    
+    """
+
+    fig = raw.pick(['meg', 'eeg']).plot(n_channels=np.inf, duration=raw.times[-1])
+
+    if savebase is not None:
+        figname = savebase.format('rawdata')
+        fig.savefig(figname, dpi=150, transparent=True)
+        plt.close(fig)
+
+        # Return the filename
+        savebase = pathlib.Path(savebase)
+        filebase = savebase.parent.name + "/" + savebase.name
+        fpath = filebase.format('rawdata')
+    else:
+        fpath = None
+    return fpath
+
+
 def plot_channel_time_series(raw, savebase=None, exclude_bads=False):
     """Plots sum-square time courses.
     
diff --git a/osl/report/templates/raw_subject_panel.html b/osl/report/templates/raw_subject_panel.html
index 901923e1..62e43380 100644
--- a/osl/report/templates/raw_subject_panel.html
+++ b/osl/report/templates/raw_subject_panel.html
@@ -49,6 +49,10 @@ <h3>{{ data.fif_id }} &ensp; ({{ data.num }} of {{ data.total }})</h3>
     </div>
     
     <div class="tabpage" style="width: 100%; display: none" id={{ data.fif_id }}_timeseries>
+        <div style="width: 100%">
+            <h4>Raw data</h4>
+            <img src="{{ data.plt_rawdata }}" alt="" style='max-width: 60%'/>
+        </div>
         {% if data.bad_seg != [] %}
             <div style="width: 100%">
                 <h4>Bad segments</h4>

From 52f7874c7e636c0bb430c9d6b617eeeac1daacdd Mon Sep 17 00:00:00 2001
From: matsvanes <mats.vanes@psych.ox.ac.uk>
Date: Sat, 20 Jan 2024 11:44:38 +0000
Subject: [PATCH 05/11] replace legacy raw.plot_psd() with
 raw.compute_psd().plot()

---
 osl/report/preproc_report.py | 28 +++++++++++++---------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/osl/report/preproc_report.py b/osl/report/preproc_report.py
index 29f64ae6..4fc5e4f1 100644
--- a/osl/report/preproc_report.py
+++ b/osl/report/preproc_report.py
@@ -814,13 +814,12 @@ def plot_spectra(raw, savebase=None):
             continue
 
         # Plot spectra
-        raw.plot_psd(
-            show=False,
-            picks=chan_inds,
-            ax=ax[row],
+        raw.compute_psd(
+            picks=chan_inds, 
             n_fft=int(raw.info['sfreq']*2),
-            verbose=0,
-        )
+            verbose=0).plot(
+                        axes=ax[row],
+                        show=False)
 
         ax[row].set_title(name, fontsize=12)
 
@@ -843,15 +842,14 @@ def plot_spectra(raw, savebase=None):
             continue
 
         # Plot zoomed in spectra
-        raw.plot_psd(
-            show=False,
-            picks=chan_inds,
-            ax=ax[row],
-            fmin=1,
-            fmax=48,
-            n_fft=int(raw.info['sfreq']*2),
-            verbose=0,
-        )
+        raw.compute_psd(
+        picks=chan_inds, 
+        fmin=1,
+        fmax=48,
+        n_fft=int(raw.info['sfreq']*2),
+        verbose=0).plot(
+                    axes=ax[row],
+                    show=False)
 
         ax[row].set_title(name, fontsize=12)
 

From 9be7199d23549ac25daf4191614dd0d14527773f Mon Sep 17 00:00:00 2001
From: cgohil8 <53237863+cgohil8@users.noreply.github.com>
Date: Thu, 8 Feb 2024 11:27:17 +0000
Subject: [PATCH 06/11] Improvements (#265)

* Refact: removed progress bar character limit.
* Enhanc: added a check/warning for nans in structurals.
---
 osl/source_recon/rhino/surfaces.py | 10 +++++++++-
 osl/source_recon/rhino/utils.py    |  6 ++++++
 osl/source_recon/sign_flipping.py  |  6 +++---
 3 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/osl/source_recon/rhino/surfaces.py b/osl/source_recon/rhino/surfaces.py
index 52793de1..b11e3be2 100644
--- a/osl/source_recon/rhino/surfaces.py
+++ b/osl/source_recon/rhino/surfaces.py
@@ -163,7 +163,7 @@ def compute_surfaces(
     if smri_ext not in [".nii", ".nii.gz"]:
         raise ValueError("smri_file needs to be a niftii file with a .nii or .nii.gz extension")
 
-    # Copy smri to new file for modification
+    # Copy sMRI to new file for modification
     img = nib.load(smri_file)
     nib.save(img, filenames["smri_file"])
 
@@ -234,6 +234,14 @@ def compute_surfaces(
     # -------------------------------------------------------
     # 2) Use BET to skull strip sMRI so that flirt works well
 
+    # Check sMRI doesn't contain nans (this can cause segmentation faults with FSL's bet)
+    if rhino_utils._check_nii_for_nan(filenames["smri_file"]):
+        log_or_print("WARNING: nan found in sMRI file. This might cause issues with BET.")
+        old_smri_file = Path(smri_file)
+        new_smri_file = old_smri_file.with_name(old_smri_file.stem + '_fixed' + old_smri_file.suffix)
+        log_or_print("If you encounter an error, it might be possible to fix the file with:")
+        log_or_print(f"fslmaths {old_smri_file} -nan {new_smri_file}")
+
     log_or_print("Running BET pre-FLIRT...")
 
     # Command: bet <flirt_smri_mniaxes_file> <flirt_smri_mniaxes_bet_file>
diff --git a/osl/source_recon/rhino/utils.py b/osl/source_recon/rhino/utils.py
index 92d1977b..01ec13bb 100644
--- a/osl/source_recon/rhino/utils.py
+++ b/osl/source_recon/rhino/utils.py
@@ -315,6 +315,12 @@ def _get_orient(nii_file):
     return orient
 
 
+def _check_nii_for_nan(filename):
+    img = nib.load(filename)
+    data = img.get_fdata()
+    return np.isnan(data).any()
+
+
 @cfunc(intc(CPointer(float64), intp, CPointer(float64), voidptr))
 def majority(values_ptr, len_values, result, data):
     """
diff --git a/osl/source_recon/sign_flipping.py b/osl/source_recon/sign_flipping.py
index bc3f70da..efb8e585 100644
--- a/osl/source_recon/sign_flipping.py
+++ b/osl/source_recon/sign_flipping.py
@@ -95,7 +95,7 @@ def find_flips(
 
         # Randomly permute the sign of different channels and calculate the metric
         if use_tqdm:
-            iterator = trange(n_iter, desc="sign flipping", ncols=98)
+            iterator = trange(n_iter, desc="sign flipping")
         else:
             iterator = range(n_iter)
         for j in iterator:
@@ -142,7 +142,7 @@ def load_covariances(parc_files, n_embeddings=1, standardize=True, loader=None,
     """
     covs = []
     if use_tqdm:
-        iterator = trange(len(parc_files), desc="Calculating covariances", ncols=98)
+        iterator = trange(len(parc_files), desc="Calculating covariances")
     else:
         iterator = range(len(parc_files))
     for i in iterator:
@@ -195,7 +195,7 @@ def find_template_subject(covs, diag_offset=0):
     # Calculate the similarity between subjects
     n_subjects = len(covs)
     metric = np.zeros([n_subjects, n_subjects])
-    for i in trange(n_subjects, desc="Comparing subjects", ncols=98):
+    for i in trange(n_subjects, desc="Comparing subjects"):
         for j in range(i + 1, n_subjects):
             metric[i, j] = covariance_matrix_correlation(covs[i], covs[j], diag_offset, mode="abs")
             metric[j, i] = metric[i, j]

From bb8e0b970977de46b6836065312adbb4c43c6f40 Mon Sep 17 00:00:00 2001
From: cgohil8 <53237863+cgohil8@users.noreply.github.com>
Date: Thu, 8 Feb 2024 17:48:31 +0000
Subject: [PATCH 07/11] Fixed readthedocs (#266)

---
 .readthedocs.yaml  |  2 +-
 doc/source/api.rst | 45 ++++++++++++++++++++++++++++++--------------
 doc/source/conf.py | 14 +++++++++-----
 requirements.txt   | 47 ++++++++++++++++++++++------------------------
 4 files changed, 63 insertions(+), 45 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 4a079703..0013e92f 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.8"
     # You can also specify other tool versions:
     # nodejs: "16"
     # rust: "1.55"
diff --git a/doc/source/api.rst b/doc/source/api.rst
index aa80526f..a157ce66 100644
--- a/doc/source/api.rst
+++ b/doc/source/api.rst
@@ -1,5 +1,5 @@
 API
-================
+===
 
 This page is the reference for the functions in OSL.
 
@@ -162,9 +162,11 @@ Utility functions for running an OSL Preprocessing pipeline.
 
 
 GLM
-******
+***
+
 GLM Base
 ++++++++
+
 Modality specific wrappers for glmtools.
 
 .. currentmodule:: osl.glm.glm_base
@@ -193,7 +195,7 @@ Modality specific wrappers for glmtools.
    SensorClusterPerm.get_sig_clusters
 
 GLM Epochs
-++++++++++++++++++++++++
+++++++++++
 
 .. currentmodule:: osl.glm.glm_epochs
 
@@ -227,7 +229,7 @@ GLM Epochs
 
 
 GLM Spectrum
-++++++++++++++++++++++++
+++++++++++++
 
 GLM-Spectrum classes and functions designed to work with GLM-Spectra computed from  MNE format sensorspace data
 
@@ -284,11 +286,13 @@ GLM-Spectrum classes and functions designed to work with GLM-Spectra computed fr
 
 
 RHINO
-********************
+*****
+
 Tools for Coregistration and forward modeling 
 
 Coregistration
 ++++++++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.coreg
@@ -309,6 +313,7 @@ Deep-level RHINO functions used by wrappers
 
 Forward modeling
 ++++++++++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.forward_model
@@ -324,7 +329,8 @@ Deep-level RHINO functions used by wrappers
 
 
 FSL-utils
-+++++++++++
++++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.fsl_utils
@@ -342,7 +348,8 @@ Deep-level RHINO functions used by wrappers
 
 
 Polhemus
-+++++++++++
+++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.polhemus
@@ -358,7 +365,8 @@ Deep-level RHINO functions used by wrappers
 
 
 Surfaces
-+++++++++++
+++++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.surfaces
@@ -378,7 +386,8 @@ Deep-level RHINO functions used by wrappers
 
 
 Utils
-+++++++++++
++++++
+
 Deep-level RHINO functions used by wrappers
 
 .. currentmodule:: osl.source_recon.rhino.utils
@@ -448,7 +457,7 @@ Deep-level RHINO functions used by wrappers
 
 
 Source Reconstruction
-**********************
+*********************
 
 Pipeline Functions
 ++++++++++++++++++
@@ -467,6 +476,7 @@ Primary user-level functions for running OSL coregistration and source_recon fun
 
 Wrappers
 ++++++++
+
 Primary wrapper functions to use in a source_recon configuration
 
 .. currentmodule:: osl.source_recon.wrappers
@@ -499,6 +509,7 @@ Primary wrapper functions to use in a source_recon configuration
 
 Beamforming
 +++++++++++
+
 Second-level beamforming functions used by wrappers
 
 .. currentmodule:: osl.source_recon.beamforming
@@ -533,9 +544,9 @@ Second-level beamforming functions used by wrappers
     _prepare_beamformer_input
 
 
-
 Sign-flipping
 +++++++++++++
+
 Second-level sign-flipping functions used by wrappers
 
 .. currentmodule:: osl.source_recon.sign_flipping
@@ -566,6 +577,7 @@ Second-level sign-flipping functions used by wrappers
 
 Utils
 +++++
+
 Utility functions for running an OSL Source Recon pipeline.
 
 .. currentmodule:: osl.source_recon.batch
@@ -580,6 +592,7 @@ Utility functions for running an OSL Source Recon pipeline.
 
 Parcellation
 ************
+
 Second-level Parcellation functions used by wrappers
 
 .. currentmodule:: osl.source_recon.parcellation.parcellation
@@ -620,6 +633,7 @@ Second-level Parcellation functions used by wrappers
 
 Nifti Utils
 ++++++++++++
+
 Second-level Parcellation functions used by wrappers
 
 .. currentmodule:: osl.source_recon.parcellation.nii
@@ -638,9 +652,11 @@ Second-level Parcellation functions used by wrappers
 
 Report
 ******
+
 Sensor level
 ++++++++++++
-.. currentmodule:: osl.report.raw_report
+
+.. currentmodule:: osl.report.preproc_report
 
 .. autosummary::
    :toctree: stubs
@@ -656,6 +672,7 @@ Sensor level
    
 Source level
 ++++++++++++
+
 .. currentmodule:: osl.report.src_report
 
 .. autosummary::
@@ -685,7 +702,7 @@ File handling
 
 
 Logger
-++++++++++++
+++++++
 
 .. currentmodule:: osl.utils.logger
 
@@ -735,4 +752,4 @@ OPM Utilities
 
     convert_notts
 
-    correct_mri
\ No newline at end of file
+    correct_mri
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 9938c57f..9a678b9b 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -6,14 +6,18 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import os
+import sys
+import inspect
+
+__location__ = os.path.join(
+    os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
+)
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
+sys.path.insert(0, os.path.join(__location__, "../.."))
 
 # -- Project information -----------------------------------------------------
 
diff --git a/requirements.txt b/requirements.txt
index 53dd28db..2c078455 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,36 +1,33 @@
-numpy~=1.22.2
-scipy~=1.8.0
-matplotlib~=3.5.0
-mne==1.0.0
-scikit-learn~=0.0
-fslpy
+numpy~=1.23.5
+scipy~=1.10.1
+matplotlib~=3.7.1
+mne==1.3.1
+scikit-learn~=1.2.2
+fslpy~=3.11.3
 sails>=1.4.0
 glmtools>=0.2.1
-tabulate~=0.8.9
-pyyaml>=5.1
-neurokit2
-jinja2-3.0.3
-file-tree
-pymatreader
+tabulate~=0.9.0
+pyyaml~=6.0
+neurokit2~=0.2.3
+jinja2~=3.1.2
+pandas~=1.5.3
+nilearn~=0.10.2
+nibabel~=5.0.1
+opencv-python~=4.7.0.72
+numba~=0.56.4
+parse~=1.19.0
+dask~=2023.3.2
+distributed~=2023.3.2
+
 # Docs
-sphinx==4.0.2
+sphinx
 numpydoc
 sphinx_gallery
 pydata-sphinx-theme
+
 # Dev
-setuptools>=41.0.1
+setuptools
 pytest
 pytest-cov
 coverage
 flake8
-
-#yaml~=0.2.5  # killing the docs build for some reason
-h5py~=3.6.0
-anamnesis~=1.0.3
-pandas~=1.3.5
-nilearn~=0.9.0
-nibabel~=3.2.2
-#scikit-learn~=1.0.2
-opencv-python~=4.5.5.62
-open3d==0.9.0.0
-numba~=0.53.1

From f9e1eacbe78264a9b18c615c7d2efa3e2ab42e90 Mon Sep 17 00:00:00 2001
From: cgohil8 <53237863+cgohil8@users.noreply.github.com>
Date: Fri, 9 Feb 2024 09:45:22 +0000
Subject: [PATCH 08/11] Handle sform errors in sMRI files + PSD plot fix +
 installation instructions (#267)

---
 README.md                                     |  5 +-
 doc/source/conf.py                            |  8 +--
 doc/source/install.rst                        | 26 +++++++--
 examples/extract_rhino_files.py               | 57 -------------------
 examples/fix_smri_files.py                    | 29 ++++++++++
 osl/source_recon/parcellation/parcellation.py | 14 +++--
 osl/source_recon/rhino/utils.py               | 10 +++-
 7 files changed, 74 insertions(+), 75 deletions(-)
 delete mode 100644 examples/extract_rhino_files.py
 create mode 100644 examples/fix_smri_files.py

diff --git a/README.md b/README.md
index 7b18d703..f786d7e0 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,8 @@
 OHBA Software Library (OSL)
 ===========================
 
+Documentation: https://osl.readthedocs.io/en/latest/.
+
 Install from Source Code
 ------------------------
 The recommended installation depends on your operating system. OSL can be installed from source using:
@@ -14,11 +16,10 @@ pip install -e .
 where the environment file `<os>.yml` can be:
 
 - `linux.yml` for a generic linux machine.
-- `m1_mac.yml` if you are using a modern Mac computer.
 - `hbaws.yml` if you are using an OHBA workstation at Oxford.
 - `bmrc.yml` if you are using the BMRC at Oxford.
 
-Note, all of the above environments come with Jupyter Notebook installed. The `hbaws.yml` and `m1_mac.yml` environments also comes with Spyder installed.
+Note, all of the above environments come with Jupyter Notebook installed. The `hbaws.yml` environment also comes with Spyder installed.
 
 Deleting osl
 ------------
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 9a678b9b..cddbe488 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -21,12 +21,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'osl'
-copyright = '2023, OMG'
-author = 'OMG'
+project = 'OSL'
+copyright = '2023, OHBA Analysis Group'
+author = 'OHBA Analysis Group'
 
 # The full version, including alpha/beta/rc tags
-release = '0.0.1dev'
+release = '0.5.1'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/doc/source/install.rst b/doc/source/install.rst
index 88f4ad6a..8e937f32 100644
--- a/doc/source/install.rst
+++ b/doc/source/install.rst
@@ -1,12 +1,28 @@
 Installation
 ============
 
-First, make sure you have conda (or miniconda) installed: https://docs.conda.io/en/latest. Then oslpy can be installed from source using the following:
+We recommend installing OSL within a virtual environment. You can do this with `Anaconda <https://docs.anaconda.com/free/anaconda/install/index.html>`_ (or `miniconda <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_).
 
-::
-    
-    git clone https://github.com/OHBA-analysis/oslpy.git
-    cd oslpy
+Linux
+-----
+
+1. Install FSL using the instructions `here <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux>`_.
+
+2. Install OSL either via pip using::
+
+    pip install osl
+
+or from source (in editable mode) using::
+
+    git clone https://github.com/OHBA-analysis/osl.git
+    cd osl
     conda env create -f envs/linux.yml
     conda activate osl
     pip install -e .
+
+Windows
+-------
+
+If you're using a Windows machine, we recommend you install FSL within a `Ubuntu <https://ubuntu.com/wsl>`_ (linux) subsystem following the instructions `here <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows>`_.
+
+Then install OSL using the instructions above.
diff --git a/examples/extract_rhino_files.py b/examples/extract_rhino_files.py
deleted file mode 100644
index 4abf3bc3..00000000
--- a/examples/extract_rhino_files.py
+++ /dev/null
@@ -1,57 +0,0 @@
-"""Example script for extracting previously computed surfaces and coregistration.
-
-Sometimes newer version of OSL aren't backwards compatible. This maybe an issue
-if you want to use files created with an older version of OSL. This often happens
-in the coregistration step, where you want to use previously computed surfaces
-and coregistration.
-
-In this script, we extract previously computed surfaces and the coregistation and
-create a new directory which will work for the latest version of OSL.
-
-We give example code for doing this in serial and in parallel using the batch
-processing - you don't need to do both.
-"""
-
-# ---------
-# In serial
-
-from osl.source_recon import setup_fsl
-from osl.source_recon.rhino.utils import extract_rhino_files
-
-setup_fsl("/opt/ohba/fsl/6.0.5")
-
-old_dir = "path/to/old/src/dir"
-new_dir = "src"
-
-extract_rhino_files(old_dir, new_dir)
-
-# -----------
-# In parallel
-
-from glob import glob
-from dask.distributed import Client
-
-from osl import source_recon, utils
-
-if __name__ == "__main__":
-    utils.logger.set_up(level="INFO")
-    source_recon.setup_fsl("/opt/ohba/fsl/6.0.5")
-
-    old_dir = "path/to/old/src/dir"
-    new_dir = "src"
-
-    subjects = [path.split("/")[-1] for path in sorted(glob(f"{old_dir}/sub-*"))]
-
-    config = f"""
-        source_recon:
-        - extract_rhino_files: {{old_src_dir: {old_dir}}}
-    """
-
-    client = Client(n_workers=16, threads_per_worker=1)
-
-    source_recon.run_src_batch(
-        config,
-        src_dir=new_dir,
-        subjects=subjects,
-        dask_client=True,
-    )
diff --git a/examples/fix_smri_files.py b/examples/fix_smri_files.py
new file mode 100644
index 00000000..59cb2c0e
--- /dev/null
+++ b/examples/fix_smri_files.py
@@ -0,0 +1,29 @@
+"""Fix sform code of structurals.
+
+This script uses FSL to set the sform code of any structural
+whose sform code is not 1 or 4 to make sure it is compatible
+with OSL.
+
+Warning: this script will permanently change the SMRI file.
+"""
+
+import nibabel as nib
+
+from osl import source_recon
+
+source_recon.setup_fsl("/path/to/fsl")
+
+# Paths to files to fix
+files = [
+    "smri/sub-001.nii.gz",
+    "smri/sub-002.nii.gz",
+]
+
+for file in files:
+    smri = nib.load(file)
+    sformcode = smri.header.get_sform(coded=True)[-1]
+    if sformcode not in [1, 4]:
+        cmd = f"fslorient -setsformcode 1 {file}"
+        source_recon.rhino.utils.system_call(cmd)
+
+print("Done”)
diff --git a/osl/source_recon/parcellation/parcellation.py b/osl/source_recon/parcellation/parcellation.py
index d3f1bdc5..8c4713c7 100644
--- a/osl/source_recon/parcellation/parcellation.py
+++ b/osl/source_recon/parcellation/parcellation.py
@@ -476,12 +476,16 @@ def plot_psd(parc_ts, fs, freq_range, parcellation_file, filename):
         Output filename.
     """
     if parc_ts.ndim == 3:
-        # (parcels, time, epochs) -> (parcels, time)
-        shape = parc_ts.shape
-        parc_ts = parc_ts.reshape(shape[0], shape[1] * shape[2])
+        # Calculate PSD for each epoch individually and average
+        psd = []
+        for i in range(parc_ts.shape[-1]):
+            f, p = welch(parc_ts[..., i], fs=fs)
+            psd.append(p)
+        psd = np.mean(psd, axis=0)
+    else:
+        # Calcualte PSD of continuous data
+        f, psd = welch(parc_ts, fs=fs)
 
-    # Calculate PSD
-    f, psd = welch(parc_ts, fs=fs)
     n_parcels = psd.shape[0]
 
     # Re-order to use colour to indicate anterior->posterior location
diff --git a/osl/source_recon/rhino/utils.py b/osl/source_recon/rhino/utils.py
index 01ec13bb..ee6f53c7 100644
--- a/osl/source_recon/rhino/utils.py
+++ b/osl/source_recon/rhino/utils.py
@@ -281,7 +281,10 @@ def _get_sform(nii_file):
     if sformcode == 1 or sformcode == 4:
         sform = nib.load(nii_file).header.get_sform()
     else:
-        raise ValueError("sform code for {} is {}, and needs to be 4 or 1".format(nii_file, sformcode))
+        raise ValueError(
+            f"sform code for {nii_file} is {sformcode}, and needs to be 4 or 1.\n"
+            "To fix see: https://github.com/OHBA-analysis/osl/blob/main/examples/fix_smri_files.py"
+        )
 
     sform = Transform("mri_voxel", "mri", sform)
     return sform
@@ -299,7 +302,10 @@ def _get_mni_sform(nii_file):
     if sformcode == 1 or sformcode == 4:
         sform = nib.load(nii_file).header.get_sform()
     else:
-        raise ValueError("sform code for {} is {}, and needs to be 4 or 1".format(nii_file, sformcode))
+        raise ValueError(
+            f"sform code for {nii_file} is {sformcode}, and needs to be 4 or 1.\n"
+            "To fix see: https://github.com/OHBA-analysis/osl/blob/main/examples/fix_smri_files.py"
+        )
 
     sform = Transform("unknown", "mni_tal", sform)
     return sform

From 40970ec5911580e8b8bb034be75e19fc2d99c93f Mon Sep 17 00:00:00 2001
From: cgohil8 <53237863+cgohil8@users.noreply.github.com>
Date: Mon, 12 Feb 2024 13:50:06 +0000
Subject: [PATCH 09/11] Windows install (#268)

---
 envs/{m1_mac.yml => m1-mac.yml}        |  0
 envs/{m2_mac.yml => m2-mac.yml}        |  0
 envs/windows.yml                       | 46 ++++++++++++++++++++++++++
 examples/oxford/ssp_pipeline/README.md |  4 +--
 4 files changed, 48 insertions(+), 2 deletions(-)
 rename envs/{m1_mac.yml => m1-mac.yml} (100%)
 rename envs/{m2_mac.yml => m2-mac.yml} (100%)
 create mode 100644 envs/windows.yml

diff --git a/envs/m1_mac.yml b/envs/m1-mac.yml
similarity index 100%
rename from envs/m1_mac.yml
rename to envs/m1-mac.yml
diff --git a/envs/m2_mac.yml b/envs/m2-mac.yml
similarity index 100%
rename from envs/m2_mac.yml
rename to envs/m2-mac.yml
diff --git a/envs/windows.yml b/envs/windows.yml
new file mode 100644
index 00000000..b534ebe8
--- /dev/null
+++ b/envs/windows.yml
@@ -0,0 +1,46 @@
+name: osl
+channels:
+- conda-forge
+dependencies:
+- python=3.8.16
+- pip=23.0.1
+- vtk=9.1.0=*osmesa*
+- pyvista=0.38.5
+- pip:
+  - jupyter==1.0.0
+  - ipympl==0.9.3
+  - ipywidgets==8.0.5
+  - ipyevents==2.0.1
+  - ipyvtklink==0.2.2
+  - jupyter-client==8.1.0
+  - numpy==1.23.5
+  - scipy==1.10.1
+  - matplotlib==3.7.1
+  - mne==1.3.1
+  - scikit-learn==1.2.2
+  - fslpy==3.11.3
+  - sails==1.4.0
+  - tabulate==0.9.0
+  - pyyaml==6.0
+  - neurokit2==0.2.3
+  - jinja2==3.1.2
+  - glmtools==0.2.1
+  - numba==0.56.4
+  - nilearn==0.10.2
+  - dask==2023.3.2
+  - distributed==2023.3.2
+  - parse==1.19.0
+  - opencv-python==4.7.0.72
+  - h5io==0.1.7
+  - mat73==0.60
+  - nibabel==5.0.1
+  - pandas==1.5.3
+  - panel==1.2.3
+  - pqdm==0.2.0
+  - seaborn==0.12.2
+  - tensorflow==2.9.1
+  - tensorflow_probability==0.17.0
+  - tqdm==4.65.0
+  - osfclient==0.0.5
+  - osl==0.5.1
+  - osl-dynamics==1.2.11
diff --git a/examples/oxford/ssp_pipeline/README.md b/examples/oxford/ssp_pipeline/README.md
index dce5e0cc..e113c40b 100644
--- a/examples/oxford/ssp_pipeline/README.md
+++ b/examples/oxford/ssp_pipeline/README.md
@@ -1,5 +1,5 @@
-Manual ICA Pipeline
--------------------
+SSP Pipeline
+------------
 
 The scripts in this directory contain the recommended settings for preprocessing continuous data collected using the new scanner (Neo) at OHBA, Oxford. It doesn't matter if the data was recorded during a task or at rest.
 

From ec5212cef1199b2f473755617eff622d82673f91 Mon Sep 17 00:00:00 2001
From: cgohil8 <53237863+cgohil8@users.noreply.github.com>
Date: Thu, 15 Feb 2024 09:49:48 +0000
Subject: [PATCH 10/11] Changed reference brain + beamforming regularisation
 (#270)

* Don't pin down osl/osl-dynamics version in Windows env file.
* Use same standard brain as Matlab OSL.
* Option to specify regularisation in beamforming.
* Fixed bug generating the source report (without extra functions).
---
 envs/windows.yml                |  4 ++--
 osl/report/preproc_report.py    |  6 +++---
 osl/report/src_report.py        |  3 +--
 osl/source_recon/rhino/utils.py |  4 ++--
 osl/source_recon/wrappers.py    | 10 ++++++++++
 5 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/envs/windows.yml b/envs/windows.yml
index b534ebe8..47a2193b 100644
--- a/envs/windows.yml
+++ b/envs/windows.yml
@@ -42,5 +42,5 @@ dependencies:
   - tensorflow_probability==0.17.0
   - tqdm==4.65.0
   - osfclient==0.0.5
-  - osl==0.5.1
-  - osl-dynamics==1.2.11
+  - osl
+  - osl-dynamics
diff --git a/osl/report/preproc_report.py b/osl/report/preproc_report.py
index 4fc5e4f1..ccbb63a2 100644
--- a/osl/report/preproc_report.py
+++ b/osl/report/preproc_report.py
@@ -441,9 +441,9 @@ def save_extra_funcs(raw, savebase=None):
     
     """
     extra_funcs = re.findall(
-    "%% extra_funcs start %%(.*?)%% extra_funcs end %%",
-    raw.info["description"],
-    flags=re.DOTALL,
+        "%% extra_funcs start %%(.*?)%% extra_funcs end %%",
+        raw.info["description"],
+        flags=re.DOTALL,
     )
     
     if savebase is not None:
diff --git a/osl/report/src_report.py b/osl/report/src_report.py
index cf43a1c4..6aa45b76 100644
--- a/osl/report/src_report.py
+++ b/osl/report/src_report.py
@@ -137,8 +137,7 @@ def save_extra_funcs(extra_funcs, reportdir):
     fpath : str
         Path to saved text file.
     """
-    
-    if reportdir is not None:
+    if reportdir is not None and extra_funcs is not None:
         fpath = reportdir / 'extra_funcs.txt'
         with(open(fpath, 'w')) as file:
             [print(f"{inspect.getsource(func)}\n\n", file=file) for func in extra_funcs]
diff --git a/osl/source_recon/rhino/utils.py b/osl/source_recon/rhino/utils.py
index ee6f53c7..dd36881a 100644
--- a/osl/source_recon/rhino/utils.py
+++ b/osl/source_recon/rhino/utils.py
@@ -80,7 +80,7 @@ def get_rhino_files(subjects_dir, subject):
         "bet_outskin_plus_nose_mesh_file": op.join(surfaces_dir, "outskin_plus_nose_mesh.nii.gz"),
         "bet_inskull_mesh_file": op.join(surfaces_dir, "inskull_mesh.nii.gz"),
         "bet_outskull_mesh_file": op.join(surfaces_dir, "outskull_mesh.nii.gz"),
-        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
+        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm.nii.gz"),
         "std_brain_bigfov": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm_BigFoV_facemask.nii.gz"),
         "completed": op.join(surfaces_dir, "completed.txt"),
     }
@@ -119,7 +119,7 @@ def get_rhino_files(subjects_dir, subject):
         "bet_outskin_plus_nose_mesh_file": op.join(coreg_dir, "scaled_outskin_plus_nose_mesh.nii.gz"),
         "bet_inskull_mesh_file": op.join(coreg_dir, "scaled_inskull_mesh.nii.gz"),
         "bet_outskull_mesh_file": op.join(coreg_dir, "scaled_outskull_mesh.nii.gz"),
-        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
+        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm.nii.gz"),
     }
 
     # All RHINO files
diff --git a/osl/source_recon/wrappers.py b/osl/source_recon/wrappers.py
index 5725c347..7010544e 100644
--- a/osl/source_recon/wrappers.py
+++ b/osl/source_recon/wrappers.py
@@ -411,6 +411,7 @@ def beamform(
     freq_range,
     chantypes,
     rank,
+    reg=0,
 ):
     """Wrapper function for beamforming.
 
@@ -433,6 +434,8 @@ def beamform(
         Channel types to use in beamforming.
     rank : dict
         Keys should be the channel types and the value should be the rank to use.
+    reg : float
+        The regularization for the whitened data covariance.
     """
     logger.info("beamforming")
 
@@ -470,6 +473,7 @@ def beamform(
         chantypes=chantypes,
         weight_norm="nai",
         rank=rank,
+        reg=reg,
         save_filters=True,
     )
 
@@ -485,6 +489,7 @@ def beamform(
             "beamform": True,
             "chantypes": chantypes,
             "rank": rank,
+            "reg": reg,
             "freq_range": freq_range,
             "filters_cov_plot": filters_cov_plot,
             "filters_svd_plot": filters_svd_plot,
@@ -665,6 +670,7 @@ def beamform_and_parcellate(
     spatial_resolution=None,
     reference_brain="mni",
     extra_chans="stim",
+    reg=0,
 ):
     """Wrapper function for beamforming and parcellation.
 
@@ -704,6 +710,8 @@ def beamform_and_parcellate(
     extra_chans : str or list of str
         Extra channels to include in the parc-raw.fif file. Defaults to 'stim'.
         Stim channels are always added to parc-raw.fif in addition to extra_chans.
+    reg : float
+        The regularization for the whitened data covariance in the beamforming stage.
     """
     logger.info("beamform_and_parcellate")
 
@@ -741,6 +749,7 @@ def beamform_and_parcellate(
         chantypes=chantypes,
         weight_norm="nai",
         rank=rank,
+        reg=reg,
         save_filters=True,
     )
 
@@ -823,6 +832,7 @@ def beamform_and_parcellate(
             "parcellate": True,
             "chantypes": chantypes,
             "rank": rank,
+            "reg": reg,
             "freq_range": freq_range,
             "filters_cov_plot": filters_cov_plot,
             "filters_svd_plot": filters_svd_plot,

From b397393d436825031c8e9268f8fc66af584af9dd Mon Sep 17 00:00:00 2001
From: cgohil8 <53237863+cgohil8@users.noreply.github.com>
Date: Thu, 15 Feb 2024 11:16:50 +0000
Subject: [PATCH 11/11] Revert "Changed reference brain + beamforming
 regularisation (#270)" (#271)

This reverts commit ec5212cef1199b2f473755617eff622d82673f91.
---
 envs/windows.yml                |  4 ++--
 osl/report/preproc_report.py    |  6 +++---
 osl/report/src_report.py        |  3 ++-
 osl/source_recon/rhino/utils.py |  4 ++--
 osl/source_recon/wrappers.py    | 10 ----------
 5 files changed, 9 insertions(+), 18 deletions(-)

diff --git a/envs/windows.yml b/envs/windows.yml
index 47a2193b..b534ebe8 100644
--- a/envs/windows.yml
+++ b/envs/windows.yml
@@ -42,5 +42,5 @@ dependencies:
   - tensorflow_probability==0.17.0
   - tqdm==4.65.0
   - osfclient==0.0.5
-  - osl
-  - osl-dynamics
+  - osl==0.5.1
+  - osl-dynamics==1.2.11
diff --git a/osl/report/preproc_report.py b/osl/report/preproc_report.py
index ccbb63a2..4fc5e4f1 100644
--- a/osl/report/preproc_report.py
+++ b/osl/report/preproc_report.py
@@ -441,9 +441,9 @@ def save_extra_funcs(raw, savebase=None):
     
     """
     extra_funcs = re.findall(
-        "%% extra_funcs start %%(.*?)%% extra_funcs end %%",
-        raw.info["description"],
-        flags=re.DOTALL,
+    "%% extra_funcs start %%(.*?)%% extra_funcs end %%",
+    raw.info["description"],
+    flags=re.DOTALL,
     )
     
     if savebase is not None:
diff --git a/osl/report/src_report.py b/osl/report/src_report.py
index 6aa45b76..cf43a1c4 100644
--- a/osl/report/src_report.py
+++ b/osl/report/src_report.py
@@ -137,7 +137,8 @@ def save_extra_funcs(extra_funcs, reportdir):
     fpath : str
         Path to saved text file.
     """
-    if reportdir is not None and extra_funcs is not None:
+    
+    if reportdir is not None:
         fpath = reportdir / 'extra_funcs.txt'
         with(open(fpath, 'w')) as file:
             [print(f"{inspect.getsource(func)}\n\n", file=file) for func in extra_funcs]
diff --git a/osl/source_recon/rhino/utils.py b/osl/source_recon/rhino/utils.py
index dd36881a..ee6f53c7 100644
--- a/osl/source_recon/rhino/utils.py
+++ b/osl/source_recon/rhino/utils.py
@@ -80,7 +80,7 @@ def get_rhino_files(subjects_dir, subject):
         "bet_outskin_plus_nose_mesh_file": op.join(surfaces_dir, "outskin_plus_nose_mesh.nii.gz"),
         "bet_inskull_mesh_file": op.join(surfaces_dir, "inskull_mesh.nii.gz"),
         "bet_outskull_mesh_file": op.join(surfaces_dir, "outskull_mesh.nii.gz"),
-        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm.nii.gz"),
+        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
         "std_brain_bigfov": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm_BigFoV_facemask.nii.gz"),
         "completed": op.join(surfaces_dir, "completed.txt"),
     }
@@ -119,7 +119,7 @@ def get_rhino_files(subjects_dir, subject):
         "bet_outskin_plus_nose_mesh_file": op.join(coreg_dir, "scaled_outskin_plus_nose_mesh.nii.gz"),
         "bet_inskull_mesh_file": op.join(coreg_dir, "scaled_inskull_mesh.nii.gz"),
         "bet_outskull_mesh_file": op.join(coreg_dir, "scaled_outskull_mesh.nii.gz"),
-        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm.nii.gz"),
+        "std_brain": op.join(os.environ["FSLDIR"], "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
     }
 
     # All RHINO files
diff --git a/osl/source_recon/wrappers.py b/osl/source_recon/wrappers.py
index 7010544e..5725c347 100644
--- a/osl/source_recon/wrappers.py
+++ b/osl/source_recon/wrappers.py
@@ -411,7 +411,6 @@ def beamform(
     freq_range,
     chantypes,
     rank,
-    reg=0,
 ):
     """Wrapper function for beamforming.
 
@@ -434,8 +433,6 @@ def beamform(
         Channel types to use in beamforming.
     rank : dict
         Keys should be the channel types and the value should be the rank to use.
-    reg : float
-        The regularization for the whitened data covariance.
     """
     logger.info("beamforming")
 
@@ -473,7 +470,6 @@ def beamform(
         chantypes=chantypes,
         weight_norm="nai",
         rank=rank,
-        reg=reg,
         save_filters=True,
     )
 
@@ -489,7 +485,6 @@ def beamform(
             "beamform": True,
             "chantypes": chantypes,
             "rank": rank,
-            "reg": reg,
             "freq_range": freq_range,
             "filters_cov_plot": filters_cov_plot,
             "filters_svd_plot": filters_svd_plot,
@@ -670,7 +665,6 @@ def beamform_and_parcellate(
     spatial_resolution=None,
     reference_brain="mni",
     extra_chans="stim",
-    reg=0,
 ):
     """Wrapper function for beamforming and parcellation.
 
@@ -710,8 +704,6 @@ def beamform_and_parcellate(
     extra_chans : str or list of str
         Extra channels to include in the parc-raw.fif file. Defaults to 'stim'.
         Stim channels are always added to parc-raw.fif in addition to extra_chans.
-    reg : float
-        The regularization for the whitened data covariance in the beamforming stage.
     """
     logger.info("beamform_and_parcellate")
 
@@ -749,7 +741,6 @@ def beamform_and_parcellate(
         chantypes=chantypes,
         weight_norm="nai",
         rank=rank,
-        reg=reg,
         save_filters=True,
     )
 
@@ -832,7 +823,6 @@ def beamform_and_parcellate(
             "parcellate": True,
             "chantypes": chantypes,
             "rank": rank,
-            "reg": reg,
             "freq_range": freq_range,
             "filters_cov_plot": filters_cov_plot,
             "filters_svd_plot": filters_svd_plot,