From 6f973cb96a8f75f10a6a120d140370e49269ba8b Mon Sep 17 00:00:00 2001
From: Pawel <p.markiewicz@ucl.ac.uk>
Date: Wed, 26 Jan 2022 12:04:42 +0000
Subject: [PATCH 01/14] slight output modification for bias field corr

---
 niftypet/nimpa/prc/prc.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/niftypet/nimpa/prc/prc.py b/niftypet/nimpa/prc/prc.py
index 87f70141..f96c35dc 100644
--- a/niftypet/nimpa/prc/prc.py
+++ b/niftypet/nimpa/prc/prc.py
@@ -1286,6 +1286,8 @@ def bias_field_correction(fmr, fimout='', outpath='', fcomment='_N4bias', execut
 
     if len(outdct['fim']) == 1:
         outdct['fim'] = outdct['fim'][0]
+        outdct['fmsk'] = outdct['fmsk'][0]
+        
     return outdct
 
 

From 18999106b0557d4e99aaada4382266af60187243 Mon Sep 17 00:00:00 2001
From: Pawel <p.markiewicz@ucl.ac.uk>
Date: Wed, 16 Feb 2022 00:33:34 +0000
Subject: [PATCH 02/14] added institution to DICOM properties to be extracted

---
 niftypet/nimpa/prc/imio.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/niftypet/nimpa/prc/imio.py b/niftypet/nimpa/prc/imio.py
index 81b60ab9..00495245 100644
--- a/niftypet/nimpa/prc/imio.py
+++ b/niftypet/nimpa/prc/imio.py
@@ -183,6 +183,11 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
         cmmnt = dhdr[0x0020, 0x4000].value
         log.debug('   Comments: {}'.format(cmmnt))
 
+    # > institution
+    inst = ''
+    if [0x008, 0x080] in dhdr:
+        inst = dhdr[0x008, 0x080].value
+
     prtcl = ''
     if [0x18, 0x1030] in dhdr:
         prtcl = dhdr[0x18, 0x1030].value
@@ -297,7 +302,7 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
 
     if validTs:
         mrdct = {
-            'series': srs, 'protocol': prtcl, 'units': unt, 'study_time': study_time,
+            'series': srs, 'protocol': prtcl, 'units': unt, 'study_time': study_time, 'inst':inst,
             'series_time': series_time, 'acq_time': acq_time, 'scanner_id': scanner_id, 'TR': TR,
             'TE': TE}
     # ---------------------------------------------
@@ -324,7 +329,7 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
     elif isPET:
         petdct = {
             'series': srs, 'protocol': prtcl, 'study_time': study_time, 'series_time': series_time,
-            'acq_time': acq_time, 'scanner_id': scanner_id, 'type': srs_type, 'units': unt,
+            'inst':inst, 'acq_time': acq_time, 'scanner_id': scanner_id, 'type': srs_type, 'units': unt,
             'recon': recon, 'decay_corr': decay_corr, 'dcf': dcf, 'attenuation': atten,
             'scatter': scat, 'scf': scf, 'randoms': rand, 'dose_calib': dscf, 'dead_time': dt,
             'tracer': tracer, 'total_dose': tdose, 'half_life': hlife, 'positron_fract': pfract,

From 3c8d14f3053a0996c5277417a190815e26dee312 Mon Sep 17 00:00:00 2001
From: Pawel <p.markiewicz@ucl.ac.uk>
Date: Wed, 9 Mar 2022 00:38:16 +0000
Subject: [PATCH 03/14] added MGH image file support

---
 niftypet/nimpa/__init__.py     |   4 +-
 niftypet/nimpa/prc/__init__.py |   4 +-
 niftypet/nimpa/prc/imio.py     | 109 +++++++++++++++++++++++++++++++++
 niftypet/nimpa/prc/prc.py      |   3 +-
 4 files changed, 117 insertions(+), 3 deletions(-)

diff --git a/niftypet/nimpa/__init__.py b/niftypet/nimpa/__init__.py
index dc036549..128a3988 100644
--- a/niftypet/nimpa/__init__.py
+++ b/niftypet/nimpa/__init__.py
@@ -30,7 +30,7 @@
     'centre_mass_img', 'centre_mass_corr', 'coreg_spm', 'coreg_vinci',
     'create_dir', 'create_mask', 'ct2mu',
     'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort',
-    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getnii',
+    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getmgh', 'getnii', 'mgh2nii'
     'getnii_descr', 'im_cut', 'imfill', 'imsmooth', 'iyang', 'motion_reg', 'nii_gzip',
     'nii_modify', 'nii_ugzip', 'niisort', 'orientnii', 'pet2pet_rigid', 'pick_t1w',
     'psf_gaussian', 'psf_measured', 'pvc_iyang', 'realign_mltp_spm', 'resample_fsl',
@@ -68,6 +68,8 @@
     dice_coeff,
     dice_coeff_multiclass,
     fwhm2sig,
+    getmgh,
+    mgh2nii,
     getnii,
     getnii_descr,
     im_cut,
diff --git a/niftypet/nimpa/prc/__init__.py b/niftypet/nimpa/prc/__init__.py
index a3d36665..d1859359 100644
--- a/niftypet/nimpa/prc/__init__.py
+++ b/niftypet/nimpa/prc/__init__.py
@@ -2,7 +2,7 @@
 __all__ = [
     # imio
     'array2nii', 'create_dir', 'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort', 'fwhm2sig',
-    'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip', 'niisort', 'orientnii', 'pick_t1w',
+    'mgh2nii', 'getmgh', 'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip', 'niisort', 'orientnii', 'pick_t1w',
     'time_stamp',
     # prc
     'bias_field_correction', 'centre_mass_img', 'centre_mass_corr', 'ct2mu', 'im_cut',
@@ -26,7 +26,9 @@
     dcminfo,
     dcmsort,
     fwhm2sig,
+    mgh2nii,
     getnii,
+    getmgh,
     getnii_descr,
     nii_gzip,
     nii_ugzip,
diff --git a/niftypet/nimpa/prc/imio.py b/niftypet/nimpa/prc/imio.py
index 00495245..50699f1c 100644
--- a/niftypet/nimpa/prc/imio.py
+++ b/niftypet/nimpa/prc/imio.py
@@ -5,6 +5,7 @@
 import pathlib
 import re
 import shutil
+import numbers
 from subprocess import run
 from textwrap import dedent
 
@@ -17,6 +18,7 @@
 from miutil.imio.nii import nii_ugzip  # NOQA: F401 # yapf: disable
 from miutil.imio.nii import niisort  # NOQA: F401 # yapf: disable
 
+
 # > NiftyPET resources
 from .. import resources as rs
 
@@ -50,6 +52,113 @@ def fwhm2sig(fwhm, voxsize=2.0):
     return (fwhm/voxsize) / (2 * (2 * np.log(2))**.5)
 
 
+
+def mgh2nii(fim, fout=None, output=None):
+    ''' Convert `*.mgh` or `*.mgz` FreeSurfer image to NIfTI.
+        Arguments:
+            fim: path to the input MGH file
+            fout: path to the output NIfTI file, if None then
+                  creates based on `fim` 
+            output: if not None and an applicable string it will
+            output a dictionary or an array (see below)
+        Return:
+            None: returns nothing
+            'image' or 'im': outputs just the image
+            'affine': outputs just the affine matrix
+            'all': outputs all as a dictionary
+    '''
+
+    if not os.path.isfile(fim):
+        raise ValueError('The input path is incorrect!')
+
+    # > get the image dictionary
+    mghd = getmgh(fim, output='all')
+    im = mghd['im']
+
+    # > sort out the output
+    if fout is None:
+        fout = fim.parent / (fim.name.split('.')[0]+'.nii.gz')
+
+    out = fout
+    if output=='image' or output=='im':
+        out = fout, im
+    elif output=='affine':
+        out = fout, mghd['affine']
+    elif output=='all':
+        out = mghd
+        out.update(dict(fout=fout))
+
+    array2nii(
+        mghd['im'],
+        mghd['affine'],
+        fout,
+        trnsp = (mghd['transpose'].index(0), mghd['transpose'].index(1), mghd['transpose'].index(2)),
+        flip = mghd['flip'])
+
+    return out
+
+
+def getmgh(fim, nan_replace=None, output='image'):
+    '''
+    Get image from `*.mgz` or `*.mgh` file (FreeSurfer).
+    Arguments:
+        fim: input file name for the MGH/Z image
+        output: option for choosing output: 'image', 'affine' matrix or 
+                'all' for a dictionary with all the info.
+    Return:
+        'image': outputs just the image
+        'affine': outputs just the affine matrix
+        'all': outputs all as a dictionary
+    '''
+
+    if not os.path.isfile(fim):
+        raise ValueError('The input path is incorrect!')
+
+    mgh = nib.freesurfer.load(str(fim))
+
+    if output == 'image' or output == 'all':
+        
+        imr = np.asanyarray(mgh.dataobj)
+        # replace NaNs if requested
+        if isinstance(nan_replace, numbers.Number):
+            imr[np.isnan(imr)] = nan_replace
+
+        imr = np.squeeze(imr)
+        dimno = imr.ndim
+
+        # > get orientations from the affine
+        ornt = nib.io_orientation(mgh.affine)
+        trnsp = tuple(np.flip(np.argsort(ornt[:, 0])))
+        flip = tuple(np.int8(ornt[:, 1]))
+
+        # > flip y-axis and z-axis and then transpose
+        if dimno == 4:   # dynamic
+            imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2], :], (3,) + trnsp)
+        elif dimno == 3: # static
+            imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2]], trnsp)
+
+
+        # # > voxel size
+        # voxsize = mgh.header.get('pixdim')[1:mgh.header.get('dim')[0] + 1]
+        # # > rearrange voxel size according to the orientation
+        # voxsize = voxsize[np.array(trnsp)]
+
+
+    if output == 'all':
+        out = {
+            'im': imr, 'affine': mgh.affine, 'fim': fim, 'dtype': mgh.get_data_dtype(), 'shape': imr.shape,
+            'hdr': mgh.header, 'transpose': trnsp, 'flip': flip}
+    elif output == 'image':
+        out = imr
+    elif output == 'affine':
+        out = mgh.affine
+    else:
+        raise NameError("Unrecognised output request!")
+
+    return out
+
+
+
 def getnii_descr(fim):
     '''Extracts the custom description header field to dictionary'''
     nim = nib.load(fim)
diff --git a/niftypet/nimpa/prc/prc.py b/niftypet/nimpa/prc/prc.py
index f96c35dc..e7e1c218 100644
--- a/niftypet/nimpa/prc/prc.py
+++ b/niftypet/nimpa/prc/prc.py
@@ -1286,7 +1286,8 @@ def bias_field_correction(fmr, fimout='', outpath='', fcomment='_N4bias', execut
 
     if len(outdct['fim']) == 1:
         outdct['fim'] = outdct['fim'][0]
-        outdct['fmsk'] = outdct['fmsk'][0]
+        if 'fmsk' in outdct:
+            outdct['fmsk'] = outdct['fmsk'][0]
         
     return outdct
 

From 12cb849556ed4e0ddf6c3bb7e1e1500d9c550679 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 15 Mar 2022 11:56:25 +0000
Subject: [PATCH 04/14] bump ninst

---
 pyproject.toml | 2 +-
 setup.cfg      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0a28fa3c..2d988c72 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [build-system]
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4",
-            "ninst>=0.8.0", "cuvec>=2.8.0", "miutil[cuda]>=0.4.0",
+            "ninst>=0.9.0", "cuvec>=2.8.0", "miutil[cuda]>=0.4.0",
             "scikit-build>=0.11.0", "cmake>=3.18", "ninja"]
 
 [tool.setuptools_scm]
diff --git a/setup.cfg b/setup.cfg
index d0a5c3f2..842a0746 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -39,7 +39,7 @@ setup_requires=
     setuptools>=42
     wheel
     setuptools_scm[toml]
-    ninst>=0.8.0
+    ninst>=0.9.0
     scikit-build>=0.11.0
     cmake>=3.18
     ninja

From c8fe89b84d05f37df2bbed8a4ed5334b6482fe56 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 9 May 2022 05:23:29 +0100
Subject: [PATCH 05/14] rename pydcm2niix => dcm2niix

- as per https://github.com/rordenlab/dcm2niix/pull/605
---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 842a0746..6c08b63b 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -47,7 +47,7 @@ setup_requires=
     miutil[cuda]>=0.4.0
 install_requires=
     cuvec>=2.3.1
-    pydcm2niix>=1.0.20220116
+    dcm2niix>=1.0.20220116
     dipy>=1.3.0
     miutil[nii]>=0.10.0
     nibabel>=2.4.0

From 21b3e14e787e959d7e4da0a7dee1b8b2e7e114be Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 9 May 2022 07:52:50 +0100
Subject: [PATCH 06/14] lint

---
 niftypet/nimpa/__init__.py     |  4 +--
 niftypet/nimpa/prc/__init__.py |  8 +++---
 niftypet/nimpa/prc/imio.py     | 47 +++++++++++++++-------------------
 niftypet/nimpa/prc/prc.py      |  2 +-
 4 files changed, 27 insertions(+), 34 deletions(-)

diff --git a/niftypet/nimpa/__init__.py b/niftypet/nimpa/__init__.py
index 128a3988..6c3cd3d9 100644
--- a/niftypet/nimpa/__init__.py
+++ b/niftypet/nimpa/__init__.py
@@ -30,7 +30,7 @@
     'centre_mass_img', 'centre_mass_corr', 'coreg_spm', 'coreg_vinci',
     'create_dir', 'create_mask', 'ct2mu',
     'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort',
-    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getmgh', 'getnii', 'mgh2nii'
+    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getmgh', 'getnii', 'mgh2nii',
     'getnii_descr', 'im_cut', 'imfill', 'imsmooth', 'iyang', 'motion_reg', 'nii_gzip',
     'nii_modify', 'nii_ugzip', 'niisort', 'orientnii', 'pet2pet_rigid', 'pick_t1w',
     'psf_gaussian', 'psf_measured', 'pvc_iyang', 'realign_mltp_spm', 'resample_fsl',
@@ -69,7 +69,6 @@
     dice_coeff_multiclass,
     fwhm2sig,
     getmgh,
-    mgh2nii,
     getnii,
     getnii_descr,
     im_cut,
@@ -77,6 +76,7 @@
     imsmooth,
     isub,
     iyang,
+    mgh2nii,
     motion_reg,
     nii_gzip,
     nii_modify,
diff --git a/niftypet/nimpa/prc/__init__.py b/niftypet/nimpa/prc/__init__.py
index d1859359..57463c04 100644
--- a/niftypet/nimpa/prc/__init__.py
+++ b/niftypet/nimpa/prc/__init__.py
@@ -2,8 +2,8 @@
 __all__ = [
     # imio
     'array2nii', 'create_dir', 'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort', 'fwhm2sig',
-    'mgh2nii', 'getmgh', 'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip', 'niisort', 'orientnii', 'pick_t1w',
-    'time_stamp',
+    'mgh2nii', 'getmgh', 'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip', 'niisort', 'orientnii',
+    'pick_t1w', 'time_stamp',
     # prc
     'bias_field_correction', 'centre_mass_img', 'centre_mass_corr', 'ct2mu', 'im_cut',
     'imsmooth', 'imtrimup',
@@ -26,10 +26,10 @@
     dcminfo,
     dcmsort,
     fwhm2sig,
-    mgh2nii,
-    getnii,
     getmgh,
+    getnii,
     getnii_descr,
+    mgh2nii,
     nii_gzip,
     nii_ugzip,
     niisort,
diff --git a/niftypet/nimpa/prc/imio.py b/niftypet/nimpa/prc/imio.py
index 50699f1c..79327c5d 100644
--- a/niftypet/nimpa/prc/imio.py
+++ b/niftypet/nimpa/prc/imio.py
@@ -1,11 +1,11 @@
 """image input/output functionalities."""
 import datetime
 import logging
+import numbers
 import os
 import pathlib
 import re
 import shutil
-import numbers
 from subprocess import run
 from textwrap import dedent
 
@@ -18,7 +18,6 @@
 from miutil.imio.nii import nii_ugzip  # NOQA: F401 # yapf: disable
 from miutil.imio.nii import niisort  # NOQA: F401 # yapf: disable
 
-
 # > NiftyPET resources
 from .. import resources as rs
 
@@ -52,13 +51,12 @@ def fwhm2sig(fwhm, voxsize=2.0):
     return (fwhm/voxsize) / (2 * (2 * np.log(2))**.5)
 
 
-
 def mgh2nii(fim, fout=None, output=None):
     ''' Convert `*.mgh` or `*.mgz` FreeSurfer image to NIfTI.
         Arguments:
             fim: path to the input MGH file
             fout: path to the output NIfTI file, if None then
-                  creates based on `fim` 
+                  creates based on `fim`
             output: if not None and an applicable string it will
             output a dictionary or an array (see below)
         Return:
@@ -77,23 +75,21 @@ def mgh2nii(fim, fout=None, output=None):
 
     # > sort out the output
     if fout is None:
-        fout = fim.parent / (fim.name.split('.')[0]+'.nii.gz')
+        fout = fim.parent / (fim.name.split('.')[0] + '.nii.gz')
 
     out = fout
-    if output=='image' or output=='im':
+    if output == 'image' or output == 'im':
         out = fout, im
-    elif output=='affine':
+    elif output == 'affine':
         out = fout, mghd['affine']
-    elif output=='all':
+    elif output == 'all':
         out = mghd
-        out.update(dict(fout=fout))
+        out['fout'] = fout
 
     array2nii(
-        mghd['im'],
-        mghd['affine'],
-        fout,
-        trnsp = (mghd['transpose'].index(0), mghd['transpose'].index(1), mghd['transpose'].index(2)),
-        flip = mghd['flip'])
+        mghd['im'], mghd['affine'], fout,
+        trnsp=(mghd['transpose'].index(0), mghd['transpose'].index(1), mghd['transpose'].index(2)),
+        flip=mghd['flip'])
 
     return out
 
@@ -103,7 +99,7 @@ def getmgh(fim, nan_replace=None, output='image'):
     Get image from `*.mgz` or `*.mgh` file (FreeSurfer).
     Arguments:
         fim: input file name for the MGH/Z image
-        output: option for choosing output: 'image', 'affine' matrix or 
+        output: option for choosing output: 'image', 'affine' matrix or
                 'all' for a dictionary with all the info.
     Return:
         'image': outputs just the image
@@ -117,7 +113,7 @@ def getmgh(fim, nan_replace=None, output='image'):
     mgh = nib.freesurfer.load(str(fim))
 
     if output == 'image' or output == 'all':
-        
+
         imr = np.asanyarray(mgh.dataobj)
         # replace NaNs if requested
         if isinstance(nan_replace, numbers.Number):
@@ -137,17 +133,15 @@ def getmgh(fim, nan_replace=None, output='image'):
         elif dimno == 3: # static
             imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2]], trnsp)
 
-
         # # > voxel size
         # voxsize = mgh.header.get('pixdim')[1:mgh.header.get('dim')[0] + 1]
         # # > rearrange voxel size according to the orientation
         # voxsize = voxsize[np.array(trnsp)]
 
-
     if output == 'all':
         out = {
-            'im': imr, 'affine': mgh.affine, 'fim': fim, 'dtype': mgh.get_data_dtype(), 'shape': imr.shape,
-            'hdr': mgh.header, 'transpose': trnsp, 'flip': flip}
+            'im': imr, 'affine': mgh.affine, 'fim': fim, 'dtype': mgh.get_data_dtype(),
+            'shape': imr.shape, 'hdr': mgh.header, 'transpose': trnsp, 'flip': flip}
     elif output == 'image':
         out = imr
     elif output == 'affine':
@@ -158,7 +152,6 @@ def getmgh(fim, nan_replace=None, output='image'):
     return out
 
 
-
 def getnii_descr(fim):
     '''Extracts the custom description header field to dictionary'''
     nim = nib.load(fim)
@@ -411,7 +404,7 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
 
     if validTs:
         mrdct = {
-            'series': srs, 'protocol': prtcl, 'units': unt, 'study_time': study_time, 'inst':inst,
+            'series': srs, 'protocol': prtcl, 'units': unt, 'study_time': study_time, 'inst': inst,
             'series_time': series_time, 'acq_time': acq_time, 'scanner_id': scanner_id, 'TR': TR,
             'TE': TE}
     # ---------------------------------------------
@@ -438,11 +431,11 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
     elif isPET:
         petdct = {
             'series': srs, 'protocol': prtcl, 'study_time': study_time, 'series_time': series_time,
-            'inst':inst, 'acq_time': acq_time, 'scanner_id': scanner_id, 'type': srs_type, 'units': unt,
-            'recon': recon, 'decay_corr': decay_corr, 'dcf': dcf, 'attenuation': atten,
-            'scatter': scat, 'scf': scf, 'randoms': rand, 'dose_calib': dscf, 'dead_time': dt,
-            'tracer': tracer, 'total_dose': tdose, 'half_life': hlife, 'positron_fract': pfract,
-            'radio_start_time': ttime0, 'radio_stop_time': ttime1}
+            'inst': inst, 'acq_time': acq_time, 'scanner_id': scanner_id, 'type': srs_type,
+            'units': unt, 'recon': recon, 'decay_corr': decay_corr, 'dcf': dcf,
+            'attenuation': atten, 'scatter': scat, 'scf': scf, 'randoms': rand, 'dose_calib': dscf,
+            'dead_time': dt, 'tracer': tracer, 'total_dose': tdose, 'half_life': hlife,
+            'positron_fract': pfract, 'radio_start_time': ttime0, 'radio_stop_time': ttime1}
 
         out = ['pet', tracer.lower(), srs_type.lower(), scanner_id, petdct]
 
diff --git a/niftypet/nimpa/prc/prc.py b/niftypet/nimpa/prc/prc.py
index e7e1c218..c96c7c26 100644
--- a/niftypet/nimpa/prc/prc.py
+++ b/niftypet/nimpa/prc/prc.py
@@ -1288,7 +1288,7 @@ def bias_field_correction(fmr, fimout='', outpath='', fcomment='_N4bias', execut
         outdct['fim'] = outdct['fim'][0]
         if 'fmsk' in outdct:
             outdct['fmsk'] = outdct['fmsk'][0]
-        
+
     return outdct
 
 

From aeba6d9a289169c1e4e7ddc11c980be2ae1c0728 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 9 May 2022 07:53:11 +0100
Subject: [PATCH 07/14] no install_tools

---
 setup.cfg |  3 ++-
 setup.py  | 36 ------------------------------------
 2 files changed, 2 insertions(+), 37 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 6c08b63b..1bb95103 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -47,7 +47,6 @@ setup_requires=
     miutil[cuda]>=0.4.0
 install_requires=
     cuvec>=2.3.1
-    dcm2niix>=1.0.20220116
     dipy>=1.3.0
     miutil[nii]>=0.10.0
     nibabel>=2.4.0
@@ -68,6 +67,8 @@ dev=
     pytest-timeout
     pytest-xdist
 plot=miutil[plot]
+dcm2niix=dcm2niix>=1.0.20220116
+niftyreg=niftyreg
 
 [flake8]
 max_line_length=99
diff --git a/setup.py b/setup.py
index d8af94a4..bda42974 100755
--- a/setup.py
+++ b/setup.py
@@ -50,42 +50,6 @@
 resources = cs.get_resources()
 # get the current setup, if any
 Cnt = resources.get_setup()
-# check the installation of tools
-chck_tls = tls.check_version(Cnt, chcklst=["RESPATH", "REGPATH"])
-
-# -------------------------------------------
-# NiftyPET tools:
-# -------------------------------------------
-if "sdist" not in sys.argv or any(i in sys.argv for i in ["build", "bdist", "wheel"]):
-    # NiftyReg
-    if not chck_tls["REGPATH"] or not chck_tls["RESPATH"]:
-        reply = True
-        if not gpuarch:
-            try:
-                reply = tls.query_yesno(
-                    "q> the latest compatible version of NiftyReg seems to be missing.\n"
-                    "   Do you want to install it?")
-            except BaseException:
-                pass
-
-        if reply:
-            log.info(
-                dedent("""\
-                    --------------------------------------------------------------
-                    Installing NiftyReg ...
-                    --------------------------------------------------------------"""))
-            Cnt = tls.install_tool("niftyreg", Cnt)
-    log.info(
-        dedent("""\
-            --------------------------------------------------------------
-            Installation of NiftyPET-tools is done.
-            --------------------------------------------------------------"""))
-else:
-    log.info(
-        dedent("""\
-            --------------------------------------------------------------
-            Skipping installation of NiftyPET-tools.
-            --------------------------------------------------------------"""))
 
 build_ver = ".".join(__version__.split('.')[:3]).split(".dev")[0]
 setup_kwargs = {

From e33f9f0a975a54d556017a79eda493eb88d3d991 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 9 May 2022 08:18:15 +0100
Subject: [PATCH 08/14] document optional deps

---
 README.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.rst b/README.rst
index 4598b356..7e55b4ca 100644
--- a/README.rst
+++ b/README.rst
@@ -34,6 +34,8 @@ It's also recommended (but not required) to use `conda`.
       ipykernel numpy scipy scikit-image matplotlib ipywidgets
     pip install "nimpa>=2"
 
+For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ support, use ``pip install nimpa[dcm2niix,niftyreg]>=2``.
+
 External CMake Projects
 ~~~~~~~~~~~~~~~~~~~~~~~
 

From 8b3de3180f7755f036e95953f52ae8da41a0ff2c Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 9 May 2022 08:46:53 +0100
Subject: [PATCH 09/14] niftyreg package detection

---
 niftypet/nimpa/prc/prc.py    |  1 -
 niftypet/nimpa/prc/regseg.py | 26 +++++++++++++++-----------
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/niftypet/nimpa/prc/prc.py b/niftypet/nimpa/prc/prc.py
index c96c7c26..fd6d586d 100644
--- a/niftypet/nimpa/prc/prc.py
+++ b/niftypet/nimpa/prc/prc.py
@@ -727,7 +727,6 @@ def pvc_iyang(
                 ft1w,
                 outpath=os.path.join(outpath, 'PET', 'positioning'),
                 fcomment=fcomment,
-                executable=Cnt['REGPATH'],
                 omp=multiprocessing.cpu_count() / 2,
                 rigOnly=True,
                 affDirect=False,
diff --git a/niftypet/nimpa/prc/regseg.py b/niftypet/nimpa/prc/regseg.py
index d1dcb51b..e89b252f 100644
--- a/niftypet/nimpa/prc/regseg.py
+++ b/niftypet/nimpa/prc/regseg.py
@@ -7,6 +7,7 @@
 import os
 import shutil
 import sys
+from os import fspath
 from subprocess import call
 from textwrap import dedent
 
@@ -276,7 +277,7 @@ def affine_niftyreg(
     fname_aff='',
     pickname='ref',
     fcomment='',
-    executable='',
+    executable=None,
     omp=1,
     rigOnly=False,
     affDirect=False,
@@ -294,10 +295,13 @@ def affine_niftyreg(
     fthrsh=0.05,
     verbose=True,
 ):
-
-    # check if the executable exists:
+    if not executable:
+        executable = getattr(rs, 'REGPATH', None)
+        if not executable:
+            from niftyreg import bin_path
+            executable = fspath(next(bin_path.glob("reg_aladin*")))
     if not os.path.isfile(executable):
-        raise IOError('Incorrect path to executable file for registration.')
+        raise IOError(f"executable not found:{executable}")
 
     # create a folder for images registered to ref
     if outpath != '':
@@ -377,16 +381,16 @@ def resample_niftyreg(
     fcomment='',
     pickname='ref',
     intrp=1,
-    executable='',
+    executable=None,
     verbose=True,
 ):
-
-    # check if the executable exists:
-    # if executable=='' and 'RESPATH' in Cnt and os.path.isfile(Cnt['RESPATH']):
-    #     executable = Cnt['RESPATH']
-
+    if not executable:
+        executable = getattr(rs, 'RESPATH', None)
+        if not executable:
+            from niftyreg import bin_path
+            executable = fspath(next(bin_path.glob("reg_resample*")))
     if not os.path.isfile(executable):
-        raise IOError('Incorrect path to executable file for registration.')
+        raise IOError(f"executable not found:{executable}")
 
     # > output path
     if outpath == '' and fimout != '':

From 243d73cd3d7970eb2ae5a93b1ec49efe20012f81 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 10 May 2022 06:25:00 +0100
Subject: [PATCH 10/14] make CuVec optional

---
 niftypet/nimpa/__init__.py |  5 ++++-
 pyproject.toml             |  3 ++-
 setup.cfg                  | 16 ++--------------
 setup.py                   | 25 ++++++++-----------------
 4 files changed, 16 insertions(+), 33 deletions(-)

diff --git a/niftypet/nimpa/__init__.py b/niftypet/nimpa/__init__.py
index 6c3cd3d9..d29a243a 100644
--- a/niftypet/nimpa/__init__.py
+++ b/niftypet/nimpa/__init__.py
@@ -37,7 +37,10 @@
     'resample_mltp_spm', 'resample_niftyreg', 'resample_spm', 'resample_vinci', 'resample_dipy',
     'time_stamp'] # yapf: disable
 
-from numcu import add, div, mul
+try:
+    from numcu import add, div, mul
+except ImportError:
+    pass
 from pkg_resources import resource_filename
 
 from niftypet.ninst import cudasetup as cs
diff --git a/pyproject.toml b/pyproject.toml
index 2d988c72..6582a23d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,7 @@
 [build-system]
+# cuvec>=2.8.0
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4",
-            "ninst>=0.9.0", "cuvec>=2.8.0", "miutil[cuda]>=0.4.0",
+            "ninst>=0.9.0", "cuvec-base", "miutil[cuda]>=0.4.0",
             "scikit-build>=0.11.0", "cmake>=3.18", "ninja"]
 
 [tool.setuptools_scm]
diff --git a/setup.cfg b/setup.cfg
index 1bb95103..20b20fc5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -43,21 +43,9 @@ setup_requires=
     scikit-build>=0.11.0
     cmake>=3.18
     ninja
-    cuvec>=2.8.0
+    cuvec-base
     miutil[cuda]>=0.4.0
-install_requires=
-    cuvec>=2.3.1
-    dipy>=1.3.0
-    miutil[nii]>=0.10.0
-    nibabel>=2.4.0
-    ninst>=0.4.0
-    numcu
-    numpy>=1.14
-    pydicom>=1.0.2
-    scipy
-    setuptools
-    spm12
-    # SimpleITK>=1.2.0
+# cuvec>=2.8.0
 python_requires=>=3.6
 [options.extras_require]
 dev=
diff --git a/setup.py b/setup.py
index bda42974..063b36b2 100755
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,6 @@
 import re
 import sys
 from pathlib import Path
-from textwrap import dedent
 
 from setuptools import find_packages, setup
 from setuptools_scm import get_version
@@ -24,26 +23,12 @@
 tls.check_platform()
 ext = tls.check_depends() # external dependencies
 
-if not ext["git"]:
-    raise SystemError(
-        dedent("""\
-            --------------------------------------------------------------
-            Git is not installed but is required for tools installation.
-            --------------------------------------------------------------"""))
-
 cs.resources_setup(gpu=False) # install resources.py
 try:
-    gpuarch = cs.dev_setup()  # update resources.py with a supported GPU device
+    cs.dev_setup()            # update resources.py with a supported GPU device
 except Exception as exc:
     log.error("could not set up CUDA:\n%s", exc)
-    gpuarch = None
 
-# First install third party apps for NiftyPET tools
-log.info(
-    dedent("""\
-        --------------------------------------------------------------
-        Setting up NiftyPET tools ...
-        --------------------------------------------------------------"""))
 # get the local path to NiftyPET resources.py
 path_resources = cs.path_niftypet_local()
 # if exists, import the resources and get the constants
@@ -54,13 +39,18 @@
 build_ver = ".".join(__version__.split('.')[:3]).split(".dev")[0]
 setup_kwargs = {
     "use_scm_version": True, "packages": find_packages(exclude=["tests"]),
-    "package_data": {"niftypet": ["nimpa/auxdata/*"]}}
+    "package_data": {"niftypet": ["nimpa/auxdata/*"]}, "install_requires": [
+        'dipy>=1.3.0', 'miutil[nii]>=0.10.0', 'nibabel>=2.4.0', 'ninst>=0.4.0', 'numpy>=1.14',
+        'pydicom>=1.0.2', 'scipy', 'setuptools', 'spm12']}
+# 'SimpleITK>=1.2.0'
 cmake_args = [
     f"-DNIMPA_BUILD_VERSION={build_ver}", f"-DPython3_ROOT_DIR={sys.prefix}",
     f"-DNIMPA_KERNEL_RADIUS={getattr(resources, 'RSZ_PSF_KRNL', 8)}"]
 
 try:
+    import cuvec as cu
     from skbuild import setup as sksetup
+    assert cu.include_path.is_dir()
     nvcc_arches = {"{2:d}{3:d}".format(*i) for i in dinf.gpuinfo() if i[2:4] >= (3, 5)}
     if nvcc_arches:
         cmake_args.append("-DCMAKE_CUDA_ARCHITECTURES=" + ";".join(sorted(nvcc_arches)))
@@ -68,6 +58,7 @@
     log.warning("Import or CUDA device detection error:\n%s", exc)
     setup(**setup_kwargs)
 else:
+    setup_kwargs['install_requires'].extend(["cuvec>=2.3.1", "numcu"])
     for i in (Path(__file__).resolve().parent / "_skbuild").rglob("CMakeCache.txt"):
         i.write_text(re.sub("^//.*$\n^[^#].*pip-build-env.*$", "", i.read_text(), flags=re.M))
     sksetup(cmake_source_dir="niftypet", cmake_languages=("C", "CXX", "CUDA"),

From c06190a455b9c391d401ace81a4fe4e1bda53543 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 10 May 2022 06:29:38 +0100
Subject: [PATCH 11/14] cuda option (for nipet)

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 20b20fc5..0ea1fbed 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -45,7 +45,6 @@ setup_requires=
     ninja
     cuvec-base
     miutil[cuda]>=0.4.0
-# cuvec>=2.8.0
 python_requires=>=3.6
 [options.extras_require]
 dev=
@@ -55,6 +54,7 @@ dev=
     pytest-timeout
     pytest-xdist
 plot=miutil[plot]
+cuda=cuvec>=2.3.1; numcu
 dcm2niix=dcm2niix>=1.0.20220116
 niftyreg=niftyreg
 

From 34f48805331ea421e72b9a9e705d1e0daf317f6d Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 10 May 2022 06:32:23 +0100
Subject: [PATCH 12/14] better installation note

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 7e55b4ca..666b6701 100644
--- a/README.rst
+++ b/README.rst
@@ -34,7 +34,7 @@ It's also recommended (but not required) to use `conda`.
       ipykernel numpy scipy scikit-image matplotlib ipywidgets
     pip install "nimpa>=2"
 
-For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ support, use ``pip install nimpa[dcm2niix,niftyreg]>=2``.
+For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ support, simply install them separately (``conda install dcm2niix`` and/or ``pip install niftyreg``).
 
 External CMake Projects
 ~~~~~~~~~~~~~~~~~~~~~~~

From 9aa5dcb58f6655ae8018745b887a56eeef822710 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 10 May 2022 06:39:41 +0100
Subject: [PATCH 13/14] drop PATHTOOLS

---
 .github/workflows/test.yml |  2 --
 README.rst                 | 12 ++++--------
 2 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 82a69e61..038ab33c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -69,8 +69,6 @@ jobs:
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
         upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}
-      env:
-        PATHTOOLS: ${{ github.workspace }}/NiftyPET_tools
     - id: meta
       name: Changelog
       run: |
diff --git a/README.rst b/README.rst
index 666b6701..c9c09f67 100644
--- a/README.rst
+++ b/README.rst
@@ -21,20 +21,16 @@ In order to facilitate these operations, NIMPA relies on third-party software fo
 Quick Install
 ~~~~~~~~~~~~~
 
-Note that installation prompts for setting the path to ``NiftyPET_tools``.
-This can be avoided by setting the environment variables ``PATHTOOLS``.
-It's also recommended (but not required) to use `conda`.
+Note that it's recommended (but not required) to use `conda`.
 
 .. code:: sh
 
-    # optional (Linux syntax) to avoid prompts
-    export PATHTOOLS=$HOME/NiftyPET_tools
     # cross-platform install
     conda install -c conda-forge python=3 \
-      ipykernel numpy scipy scikit-image matplotlib ipywidgets
+      ipykernel numpy scipy scikit-image matplotlib ipywidgets dcm2niix
     pip install "nimpa>=2"
 
-For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ support, simply install them separately (``conda install dcm2niix`` and/or ``pip install niftyreg``).
+For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ support, simply install them separately (``pip install dcm2niix niftyreg``).
 
 External CMake Projects
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -70,7 +66,7 @@ Licence
 Copyright 2018-21
 
 - `Pawel J. Markiewicz <https://github.com/pjmark>`__ @ University College London
-- `Casper O. da Costa-Luis <https://github.com/casperdcl>`__ @ King's College London
+- `Casper O. da Costa-Luis <https://github.com/casperdcl>`__ @ University College London/King's College London
 - `Contributors <https://github.com/NiftyPET/NIMPA/graphs/contributors>`__
 
 .. |Docs| image:: https://readthedocs.org/projects/niftypet/badge/?version=latest

From 35384a97021c5d24115037a7d7808111979195af Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 10 May 2022 08:29:01 +0100
Subject: [PATCH 14/14] another comment

---
 README.rst | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/README.rst b/README.rst
index c9c09f67..e529f29e 100644
--- a/README.rst
+++ b/README.rst
@@ -14,8 +14,6 @@ The upsampling is needed for more accurate extraction (sampling) of PET data usi
 
 PVC is needed to correct for the spill-in and spill-out of PET signal from defined ROIs (specific for any given application).
 
-In order to facilitate these operations, NIMPA relies on third-party software for image conversion from DICOM to NIfTI (dcm2niix) and image registration (NiftyReg).  The additional software is installed automatically to a user specified location.
-
 **Documentation with installation manual and tutorials**: https://niftypet.readthedocs.io/
 
 Quick Install
@@ -30,7 +28,7 @@ Note that it's recommended (but not required) to use `conda`.
       ipykernel numpy scipy scikit-image matplotlib ipywidgets dcm2niix
     pip install "nimpa>=2"
 
-For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ support, simply install them separately (``pip install dcm2niix niftyreg``).
+For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ (image conversion from DICOM to NIfTI) and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ (image registration) support, simply install them separately (``pip install dcm2niix niftyreg``).
 
 External CMake Projects
 ~~~~~~~~~~~~~~~~~~~~~~~