diff --git a/.github/workflows/comment-bot.yml b/.github/workflows/comment-bot.yml
index 4451632..b44ee7b 100644
--- a/.github/workflows/comment-bot.yml
+++ b/.github/workflows/comment-bot.yml
@@ -29,6 +29,7 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "eyes"})
+        github-token: ${{ secrets.GH_TOKEN }}
     - name: Tag Commit
       run: |
         git clone https://${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY} repo
@@ -48,3 +49,4 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "rocket"})
+        github-token: ${{ secrets.GH_TOKEN }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7fd515b..f9a0ce5 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -57,8 +57,6 @@ jobs:
     - if: startsWith(matrix.python, '2')
       run: pytest
     - run: codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   matlab:
     if: github.event_name != 'pull_request' || github.head_ref != 'devel'
     runs-on: [self-hosted, python, matlab]
@@ -72,8 +70,6 @@ jobs:
     - run: pip install -U .[dev]
     - run: pytest --durations-min=1
     - run: codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     - name: Post Run setup-python
       run: setup-python -p3.7 -Dr
       if: ${{ always() }}
@@ -89,37 +85,23 @@ jobs:
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
-        build: true
+        pip: true
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
-        upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }}
-    - name: Changelog
-      run: git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      id: create_release
-      uses: actions/create-release@v1
+        upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}
+    - id: meta
+      name: Changelog
+      run: |
+        echo ::set-output name=tag::${GITHUB_REF#refs/tags/}
+        git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
+    - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: softprops/action-gh-release@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
-        tag_name: ${{ github.ref }}
-        release_name: spm12 ${{ github.ref }} beta
+        name: spm12 ${{ steps.meta.outputs.tag }} beta
         body_path: _CHANGES.md
         draft: true
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
-      with:
-        upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: dist/${{ steps.dist.outputs.whl }}
-        asset_name: ${{ steps.dist.outputs.whl }}
-        asset_content_type: application/zip
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
-      with:
-        upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: dist/${{ steps.dist.outputs.whl_asc }}
-        asset_name: ${{ steps.dist.outputs.whl_asc }}
-        asset_content_type: text/plain
+        files: |
+          dist/${{ steps.dist.outputs.whl }}
+          dist/${{ steps.dist.outputs.whl_asc }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2fcbb14..8d77ba8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.0.1
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -26,19 +26,20 @@ repos:
     exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
     args: [-i]
 - repo: https://gitlab.com/pycqa/flake8
-  rev: 3.8.4
+  rev: 3.9.2
   hooks:
   - id: flake8
+    args: [-j8]
     additional_dependencies:
     - flake8-bugbear
     - flake8-comprehensions
     - flake8-debugger
     - flake8-string-format
 - repo: https://github.com/psf/black
-  rev: 19.10b0
+  rev: 21.7b0
   hooks:
   - id: black
 - repo: https://github.com/PyCQA/isort
-  rev: 5.7.0
+  rev: 5.9.3
   hooks:
   - id: isort
diff --git a/setup.cfg b/setup.cfg
index 89f3898..3a4310a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -63,6 +63,8 @@ demo=
 [options.entry_points]
 console_scripts =
     spm12=spm12.cli:main
+[options.packages.find]
+exclude=tests
 [options.package_data]
 *=*.md, *.rst, *.m
 
diff --git a/spm12/coreg_spm_m.m b/spm12/amypad_coreg.m
similarity index 87%
rename from spm12/coreg_spm_m.m
rename to spm12/amypad_coreg.m
index 98aabcb..ae8199d 100644
--- a/spm12/coreg_spm_m.m
+++ b/spm12/amypad_coreg.m
@@ -1,4 +1,4 @@
-function [M, x] = coreg_spm_m(imref, imflo, costfun, sep, tol, fwhm, params, graphics, visual)
+function [M, x] = amypad_coreg(imref, imflo, costfun, sep, tol, fwhm, params, graphics, visual)
     if visual>0
         Fgraph = spm_figure('GetWin','Graphics');
         Finter = spm_figure('GetWin','Interactive');
diff --git a/spm12/amypad_coreg_modify_affine.m b/spm12/amypad_coreg_modify_affine.m
new file mode 100644
index 0000000..569f74c
--- /dev/null
+++ b/spm12/amypad_coreg_modify_affine.m
@@ -0,0 +1,7 @@
+function out = amypad_coreg_modify_affine(imflo, M)
+    VF = strcat(imflo,',1');
+    MM = zeros(4,4);
+    MM(:,:) = spm_get_space(VF);
+    spm_get_space(VF, M\MM(:,:));
+    out = 0;
+end
diff --git a/spm12/amypad_normw.m b/spm12/amypad_normw.m
new file mode 100644
index 0000000..f7570a5
--- /dev/null
+++ b/spm12/amypad_normw.m
@@ -0,0 +1,10 @@
+function out = amypad_normw(def_file, flist4norm)
+    job.subj.def = {def_file};
+    job.subj.resample = flist4norm;
+    job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
+    job.woptions.vox = [2, 2, 2];
+    job.woptions.interp = 4;
+    job.woptions.prefix = 'w';
+    spm_run_norm(job);
+    out=0;
+end
diff --git a/spm12/resample_spm_m.m b/spm12/amypad_resample.m
similarity index 85%
rename from spm12/resample_spm_m.m
rename to spm12/amypad_resample.m
index e58bc8c..c942f85 100644
--- a/spm12/resample_spm_m.m
+++ b/spm12/amypad_resample.m
@@ -1,4 +1,4 @@
-function out = resample_spm_m(imref, imflo, M, f_mask, f_mean, f_interp, f_which, f_prefix)
+function out = amypad_resample(imref, imflo, M, f_mask, f_mean, f_interp, f_which, f_prefix)
     %-Reslicing parameters
     rflags.mask = f_mask;
     rflags.mean = f_mean;
diff --git a/spm12/amypad_seg.m b/spm12/amypad_seg.m
new file mode 100644
index 0000000..42bf585
--- /dev/null
+++ b/spm12/amypad_seg.m
@@ -0,0 +1,46 @@
+function [param,invdef,fordef] = amypad_seg(f_mri, spm_path, nat_gm, nat_wm, nat_csf, store_fwd, store_inv, visual)
+    job.channel.vols = {strcat(f_mri,',1')};
+    job.channel.biasreg = 0.001;
+    job.channel.biasfwhm = 60;
+    job.channel.write = [0, 0];
+    job.tissue(1).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,1']};
+    job.tissue(1).ngaus = 1;
+    job.tissue(1).native = [nat_gm, 0];
+    job.tissue(1).warped = [0, 0];
+    job.tissue(2).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,2']};
+    job.tissue(2).ngaus = 1;
+    job.tissue(2).native = [nat_wm, 0];
+    job.tissue(2).warped = [0, 0];
+    job.tissue(3).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,3']};
+    job.tissue(3).ngaus = 2;
+    job.tissue(3).native = [nat_csf, 0];
+    job.tissue(3).warped = [0, 0];
+    job.tissue(4).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,4']};
+    job.tissue(4).ngaus = 3;
+    job.tissue(4).native = [0, 0];
+    job.tissue(4).warped = [0, 0];
+    job.tissue(5).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,5']};
+    job.tissue(5).ngaus = 4;
+    job.tissue(5).native = [0, 0];
+    job.tissue(5).warped = [0, 0];
+    job.tissue(6).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,6']};
+    job.tissue(6).ngaus = 2;
+    job.tissue(6).native = [0, 0];
+    job.tissue(6).warped = [0, 0];
+    job.warp.mrf = 1;
+    job.warp.cleanup = 1;
+    job.warp.reg = [0, 0.001, 0.5, 0.05, 0.2];
+    job.warp.affreg = 'mni';
+    job.warp.fwhm = 0;
+    job.warp.samp = 3;
+    job.warp.write = [store_fwd, store_inv];
+    if visual>0
+        Finter = spm_figure('GetWin','Interactive');
+    end
+    spm_jobman('initcfg');
+    segout = spm_preproc_run(job);
+    param  = segout.param{1};
+    invdef = segout.invdef{1};
+    fordef = segout.fordef{1};
+    %disp(segout);
+end
diff --git a/spm12/regseg.py b/spm12/regseg.py
index ca5ce31..5d5983b 100644
--- a/spm12/regseg.py
+++ b/spm12/regseg.py
@@ -1,6 +1,7 @@
 import errno
 import logging
 import os
+import re
 import shutil
 from textwrap import dedent
 
@@ -9,12 +10,28 @@
 from miutil import create_dir, hasext
 from miutil.imio import nii
 
-from .utils import ensure_spm
+from .utils import ensure_spm, spm_dir
 
 __author__ = ("Pawel J. Markiewicz", "Casper O. da Costa-Luis")
 log = logging.getLogger(__name__)
 
 
+def move_files(fin, opth):
+    """
+    Move input file path fin to the output folder opth.
+    """
+    fdst = os.path.join(opth, os.path.basename(fin))
+    shutil.move(fin, fdst)
+    return fdst
+
+
+def glob_match(pttrn, pth):
+    """
+    glob with regular expressions
+    """
+    return (os.path.join(pth, f) for f in os.listdir(pth) if re.match(pttrn, f))
+
+
 def fwhm2sig(fwhm, voxsize=2.0):
     return fwhm / (voxsize * (8 * np.log(2)) ** 0.5)
 
@@ -25,14 +42,13 @@ def smoothim(fim, fwhm=4, fout=""):
     """
     imd = nii.getnii(fim, output="all")
     imsmo = ndi.filters.gaussian_filter(
-        imd["im"], fwhm2sig(fwhm, voxsize=imd["voxsize"]), mode="mirror"
+        imd["im"], fwhm2sig(fwhm, voxsize=imd["voxsize"]), mode="constant"
     )
-
     if not fout:
-        fout = "{f[0]}{f[1]}_smo{fwhm}{f[2]}".format(
-            f=nii.file_parts(fim), fwhm=str(fwhm).replace(".", "-")
+        f = nii.file_parts(fim)
+        fout = os.path.join(
+            f[0], "{}_smo{}{}".format(f[1], str(fwhm).replace(".", "-"), f[2])
         )
-
     nii.array2nii(
         imsmo,
         imd["affine"],
@@ -44,7 +60,6 @@ def smoothim(fim, fwhm=4, fout=""):
         ),
         flip=imd["flip"],
     )
-
     return {"im": imsmo, "fim": fout, "fwhm": fwhm, "affine": imd["affine"]}
 
 
@@ -68,7 +83,18 @@ def coreg_spm(
     del_uncmpr=True,
     save_arr=True,
     save_txt=True,
+    modify_nii=False,
 ):
+    """Rigid body registration using SPM coreg function.
+    Args:
+      imref: reference image
+      imflo: floating image
+      fwhm_ref: FWHM of the smoothing kernel for the reference image
+      fwhm_flo: FWHM of the smoothing kernel for the reference image
+      modify_nii: modifies the affine of the NIfTI file of the floating
+        image according to the rigid body transformation.
+    """
+    out = {}  # output dictionary
     sep = sep or [4, 2]
     tol = tol or [
         0.0200,
@@ -96,7 +122,7 @@ def coreg_spm(
     log.debug("output path:%s", opth)
     create_dir(opth)
 
-    # > decompress ref image as necessary
+    # decompress ref image as necessary
     if hasext(imref, "gz"):
         imrefu = nii.nii_ugzip(imref, outpath=opth)
     else:
@@ -106,8 +132,7 @@ def coreg_spm(
 
     if fwhm_ref > 0:
         smodct = smoothim(imrefu, fwhm_ref)
-
-        # > delete the previous version (non-smoothed)
+        # delete the previous version (non-smoothed)
         os.remove(imrefu)
         imrefu = smodct["fim"]
 
@@ -117,7 +142,7 @@ def coreg_spm(
             )
         )
 
-    # > floating
+    # floating
     if hasext(imflo, "gz"):
         imflou = nii.nii_ugzip(imflo, outpath=opth)
     else:
@@ -127,8 +152,13 @@ def coreg_spm(
 
     if fwhm_flo > 0:
         smodct = smoothim(imflou, fwhm_flo)
-        # > delete the previous version (non-smoothed)
-        os.remove(imflou)
+        # delete the previous version (non-smoothed)
+        if not modify_nii:
+            os.remove(imflou)
+        else:
+            # save the uncompressed and unsmoothed version
+            imflou_ = imflou
+
         imflou = smodct["fim"]
 
         log.info(
@@ -137,10 +167,10 @@ def coreg_spm(
             )
         )
 
-    # run the matlab SPM coregistration
+    # run the MATLAB SPM registration
     import matlab as ml
 
-    Mm, xm = eng.coreg_spm_m(
+    Mm, xm = eng.amypad_coreg(
         imrefu,
         imflou,
         costfun,
@@ -153,6 +183,11 @@ def coreg_spm(
         nargout=2,
     )
 
+    # modify the affine of the floating image (as usually done in SPM)
+    if modify_nii:
+        eng.amypad_coreg_modify_affine(imflou_, Mm)
+        out["freg"] = imflou_
+
     # get the affine matrix
     M = np.array(Mm._data.tolist())
     M = M.reshape(4, 4).T
@@ -167,7 +202,6 @@ def coreg_spm(
 
     create_dir(os.path.join(opth, "affine-spm"))
 
-    # ---------------------------------------------------------------------------
     if fname_aff == "":
         if pickname == "ref":
             faff = os.path.join(
@@ -181,30 +215,26 @@ def coreg_spm(
                 "affine-spm",
                 "affine-flo-" + nii.file_parts(imflo)[1] + fcomment + ".npy",
             )
-
     else:
-
-        # > add '.npy' extension if not in the affine output file name
+        # add '.npy' extension if not in the affine output file name
         if not fname_aff.endswith(".npy"):
             fname_aff += ".npy"
 
         faff = os.path.join(opth, "affine-spm", fname_aff)
-    # ---------------------------------------------------------------------------
 
-    # > safe the affine transformation
+    # save the affine transformation
     if save_arr:
         np.save(faff, M)
     if save_txt:
         faff = os.path.splitext(faff)[0] + ".txt"
         np.savetxt(faff, M)
 
-    return {
-        "affine": M,
-        "faff": faff,
-        "rotations": x[3:],
-        "translations": x[:3],
-        "matlab_eng": eng,
-    }
+    out["affine"] = M
+    out["faff"] = faff
+    out["rotations"] = x[3:]
+    out["translations"] = x[:3]
+    out["matlab_eng"] = eng
+    return out
 
 
 def resample_spm(
@@ -245,7 +275,7 @@ def resample_spm(
     log.debug("output path:%s", opth)
     create_dir(opth)
 
-    # > decompress if necessary
+    # decompress if necessary
     if hasext(imref, "gz"):
         imrefu = nii.nii_ugzip(imref, outpath=opth)
     else:
@@ -253,7 +283,7 @@ def resample_spm(
         imrefu = os.path.join(opth, fnm)
         shutil.copyfile(imref, imrefu)
 
-    # > floating
+    # floating
     if hasext(imflo, "gz"):
         imflou = nii.nii_ugzip(imflo, outpath=opth)
     else:
@@ -280,7 +310,7 @@ def resample_spm(
     # run the Matlab SPM resampling
     import matlab as ml
 
-    eng.resample_spm_m(
+    eng.amypad_resample(
         imrefu, imflou, ml.double(M.tolist()), mask, mean, intrp, which, prefix
     )
 
@@ -297,16 +327,18 @@ def resample_spm(
     if del_out_uncmpr:
         os.remove(fim)
 
-    # > the compressed output naming
+    # the compressed output naming
     if fimout:
         fout = os.path.join(opth, fimout)
     elif pickname == "ref":
         fout = os.path.join(
-            opth, "affine_ref-" + nii.file_parts(imrefu)[1] + fcomment + ".nii.gz",
+            opth,
+            "affine_ref-" + nii.file_parts(imrefu)[1] + fcomment + ".nii.gz",
         )
     elif pickname == "flo":
         fout = os.path.join(
-            opth, "affine_flo-" + nii.file_parts(imflo)[1] + fcomment + ".nii.gz",
+            opth,
+            "affine_flo-" + nii.file_parts(imflo)[1] + fcomment + ".nii.gz",
         )
     # change the file name
     os.rename(fim + ".gz", fout)
@@ -320,3 +352,91 @@ def resample_spm(
         )
 
     return fout
+
+
+def seg_spm(
+    f_mri,
+    spm_path=None,
+    matlab_eng_name="",
+    outpath=None,
+    store_nat_gm=False,
+    store_nat_wm=False,
+    store_nat_csf=False,
+    store_fwd=False,
+    store_inv=False,
+    visual=False,
+):
+    """
+    Normalisation/segmentation using SPM12.
+    Args:
+      f_mri: file path to the T1w MRI file
+      spm_path(str): SPM path
+      matlab_eng_name: name of the Python engine for Matlab.
+      outpath: output folder path for the normalisation file output
+      store_nat_*: stores native space segmentation output for either
+        grey matter, white matter or CSF
+      sotre_fwd/inv: stores forward/inverse normalisation definitions
+      visual: shows the Matlab window progress
+    """
+    out = {}  # output dictionary
+    # get Matlab engine or use the provided one
+    eng = ensure_spm(matlab_eng_name)
+    if not spm_path:
+        spm_path = spm_dir()
+    # run SPM normalisation/segmentation
+    param, invdef, fordef = eng.amypad_seg(
+        f_mri,
+        str(spm_path),
+        float(store_nat_gm),
+        float(store_nat_wm),
+        float(store_nat_csf),
+        float(store_fwd),
+        float(store_inv),
+        float(visual),
+        nargout=3,
+    )
+    if outpath is not None:
+        create_dir(outpath)
+        out["param"] = move_files(param, outpath)
+        out["invdef"] = move_files(invdef, outpath)
+        out["fordef"] = move_files(fordef, outpath)
+        # go through tissue types and move them to the output folder
+        for c in glob_match(r"c\d*", os.path.dirname(param)):
+            nm = os.path.basename(c)[:2]
+            out[nm] = move_files(c, outpath)
+    else:
+        out["param"] = param
+        out["invdef"] = invdef
+        out["fordef"] = fordef
+
+        for c in glob_match(r"c\d*", os.path.dirname(param)):
+            nm = os.path.basename(c)[:2]
+            out[nm] = c
+    return out
+
+
+def normw_spm(f_def, files4norm, matlab_eng_name="", outpath=None):
+    """
+    Write normalisation output to NIfTI files using SPM12.
+    Args:
+      f_def: NIfTI file of definitions for non-rigid normalisation
+      files4norm: list of input NIfTI file paths in format ['file, 1']
+      matlab_eng_name: name of the Python engine for Matlab.
+      outpath: output folder path for the normalisation files
+    """
+    eng = ensure_spm(matlab_eng_name)  # get_matlab
+    eng.amypad_normw(f_def, files4norm)
+    out = []  # output list
+    if outpath is not None:
+        create_dir(outpath)
+        for f in files4norm:
+            fpth = f.split(",")[0]
+            out.append(
+                move_files(
+                    os.path.join(os.path.dirname(fpth), "w" + os.path.basename(fpth)),
+                    outpath,
+                )
+            )
+    else:
+        out.append("w" + os.path.basename(f.split(",")[0]))
+    return out
diff --git a/spm12/utils.py b/spm12/utils.py
index da67894..afbadbb 100644
--- a/spm12/utils.py
+++ b/spm12/utils.py
@@ -13,7 +13,7 @@
 except ImportError:  # fix py2.7
     from backports.functools_lru_cache import lru_cache
 
-__all__ = ["get_matlab", "ensure_spm"]
+__all__ = ["ensure_spm", "get_matlab", "spm_dir"]
 PATH_M = resource_filename(__name__, "")
 log = logging.getLogger(__name__)
 
@@ -26,14 +26,19 @@ def get_matlab(name=None):
     return eng
 
 
+def spm_dir(cache="~/.spm12", version=12):
+    cache = path.expanduser(cache)
+    if str(version) != "12":
+        raise NotImplementedError
+    return path.join(cache, "spm12")
+
+
 @lru_cache()
 @wraps(get_matlab)
 def ensure_spm(name=None, cache="~/.spm12", version=12):
     eng = get_matlab(name)
     cache = path.expanduser(cache)
-    if str(version) != "12":
-        raise NotImplementedError
-    addpath = path.join(cache, "spm12")
+    addpath = spm_dir(cache=cache, version=version)
     if path.exists(addpath):
         eng.addpath(addpath)
     if not eng.exist("spm_jobman"):
diff --git a/tests/test_regseg.py b/tests/test_regseg.py
index a3865e8..002cc87 100644
--- a/tests/test_regseg.py
+++ b/tests/test_regseg.py
@@ -34,7 +34,14 @@ def assert_equal_arrays(x, y, nmse_tol=0, denan=True):
         y: {:.3g}/{:.3g}/{:.3g}({:.3g})
         """
         ).format(
-            x.min(), x.mean(), x.max(), x.std(), y.min(), y.mean(), y.max(), y.std(),
+            x.min(),
+            x.mean(),
+            x.max(),
+            x.std(),
+            y.min(),
+            y.mean(),
+            y.max(),
+            y.std(),
         )
     )