antspymm 1.4.0__py3-none-any.whl → 1.4.2__py3-none-any.whl

antspymm/__init__.py

@@ -130,5 +130,6 @@ from .mm import mm_match_by_qc_scoring
 from .mm import mm_match_by_qc_scoring_all
 from .mm import fix_LR_RL_stuff
 from .mm import segment_timeseries_by_bvalue
+from .mm import shorten_pymm_names
 
 

antspymm/mm.py

@@ -2707,7 +2707,7 @@ def template_figure_with_overlay(scalar_label_df, prefix, outputfilename=None, t
     toviz = temp['overlay']
     return { "underlay": seggm, 'overlay': toviz, 'seg': tcrop  }
 
-def get_data( name=None, force_download=False, version=23, target_extension='.csv' ):
+def get_data( name=None, force_download=False, version=25, target_extension='.csv' ):
     """
     Get ANTsPyMM data filename
 
@@ -10219,7 +10219,7 @@ def remove_volumes_from_timeseries(time_series, volumes_to_remove):
     volumes_to_keep = [i for i in range(time_series.shape[3]) if i not in volumes_to_remove]
 
     # Select the volumes to keep
-    filtered_time_series = ants.from_numpy( time_series[..., volumes_to_keep] )
+    filtered_time_series = ants.from_numpy( time_series.numpy()[..., volumes_to_keep] )
 
     return ants.copy_image_info( time_series, filtered_time_series )
 
@@ -10654,7 +10654,136 @@ def novelty_detection_quantile(df_train, df_test):
         myqs[mykey] = abs( temp - 0.5 ) / 0.5
     return myqs
 
-def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_image, overlay_cmap='bwr', nslices=21, ncol=7, edge_image_dilation = 0, black_bg=True, axes = [0,1,2], fixed_overlay_range=None, crop=5, verbose=0 ):
+
+
+def shorten_pymm_names(x):
+    """
+    Shortens pmymm names by applying a series of regex substitutions.
+    
+    Parameters:
+    x (str): The input string to be shortened
+    
+    Returns:
+    str: The shortened string
+    """
+    xx = x.lower()
+    xx = re.sub("_", ".", xx)  # Replace underscores with periods
+    xx = re.sub("\.\.", ".", xx, flags=re.I)  # Replace double dots with single dot
+    # Apply the following regex substitutions in order
+    xx = re.sub("sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.","ilf.and.ifo", xx, flags=re.I)
+    xx = re.sub(r"sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.", "ilf.and.ifo", xx, flags=re.I)
+    xx = re.sub(r".cres.stria.terminalis.can.not.be.resolved.with.current.resolution.", "", 
+xx, flags=re.I)
+    xx = re.sub("_", ".", xx)  # Replace underscores with periods
+    xx = re.sub(r"longitudinal.fasciculus", "l.fasc", xx, flags=re.I)
+    xx = re.sub(r"corona.radiata", "cor.rad", xx, flags=re.I)
+    xx = re.sub("central", "cent", xx, flags=re.I)
+    xx = re.sub(r"deep.cit168", "dp.", xx, flags=re.I)
+    xx = re.sub("cit168", "", xx, flags=re.I)
+    xx = re.sub(".include", "", xx, flags=re.I)
+    xx = re.sub("mtg.sn", "", xx, flags=re.I)
+    xx = re.sub("brainstem", ".bst", xx, flags=re.I)
+    xx = re.sub(r"rsfmri.", "rsf.", xx, flags=re.I)
+    xx = re.sub(r"dti.mean.fa.", "dti.fa.", xx, flags=re.I)
+    xx = re.sub("perf.cbf.mean.", "cbf.", xx, flags=re.I)
+    xx = re.sub(".jhu.icbm.labels.1mm", "", xx, flags=re.I)
+    xx = re.sub(".include.optic.radiation.", "", xx, flags=re.I)
+    xx = re.sub("\.\.", ".", xx, flags=re.I)  # Replace double dots with single dot
+    xx = re.sub("\.\.", ".", xx, flags=re.I)  # Replace double dots with single dot
+    xx = re.sub("cerebellar.peduncle", "cereb.ped", xx, flags=re.I)
+    xx = re.sub(r"anterior.limb.of.internal.capsule", "ant.int.cap", xx, flags=re.I)
+    xx = re.sub(r"posterior.limb.of.internal.capsule", "post.int.cap", xx, flags=re.I)
+    xx = re.sub("t1hier.", "t1.", xx, flags=re.I)
+    xx = re.sub("anterior", "ant", xx, flags=re.I)
+    xx = re.sub("posterior", "post", xx, flags=re.I)
+    xx = re.sub("inferior", "inf", xx, flags=re.I)
+    xx = re.sub("superior", "sup", xx, flags=re.I)
+    xx = re.sub(r"dktcortex", ".ctx", xx, flags=re.I)
+    xx = re.sub(".lravg", "", xx, flags=re.I)
+    xx = re.sub("dti.mean.fa", "dti.fa", xx, flags=re.I)
+    xx = re.sub(r"retrolenticular.part.of.internal", "rent.int.cap", xx, flags=re.I)
+    xx = re.sub(r"iculus.could.be.a.part.of.ant.internal.capsule", "", xx, flags=re.I)  # Twice
+    xx = re.sub(".fronto.occipital.", ".frnt.occ.", xx, flags=re.I)
+    xx = re.sub(r".longitidinal.fasciculus.", ".long.fasc.", xx, flags=re.I)  # Twice
+    xx = re.sub(".external.capsule", ".ext.cap", xx, flags=re.I)
+    xx = re.sub("of.internal.capsule", ".int.cap", xx, flags=re.I)
+    xx = re.sub("fornix.cres.stria.terminalis", "fornix.", xx, flags=re.I)
+    xx = re.sub("capsule", "", xx, flags=re.I)
+    xx = re.sub("and.inf.frnt.occ.fasciculus.", "", xx, flags=re.I)
+    xx = re.sub("crossing.tract.a.part.of.mcp.", "", xx, flags=re.I)
+    return xx[:40]  # Truncate to first 40 characters
+
+
+def shorten_pymm_names2(x, verbose=False ):
+    """
+    Shortens pmymm names by applying a series of regex substitutions.
+
+    Parameters:
+    x (str): The input string to be shortened
+
+    verbose (bool): explain the patterns and replacements and their impact
+
+    Returns:
+    str: The shortened string
+    """
+    # Define substitution patterns as tuples
+    substitutions = [
+        ("_", "."),  
+        ("\.\.", "."),
+        ("sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.","ilf.and.ifo"),
+        (r"sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.", "ilf.and.ifo"),
+        (r".cres.stria.terminalis.can.not.be.resolved.with.current.resolution.", ""),
+        ("_", "."),
+        (r"longitudinal.fasciculus", "l.fasc"),
+        (r"corona.radiata", "cor.rad"),
+        ("central", "cent"),
+        (r"deep.cit168", "dp."),
+        ("cit168", ""),
+        (".include", ""),
+        ("mtg.sn", ""),
+        ("brainstem", ".bst"),
+        (r"rsfmri.", "rsf."),
+        (r"dti.mean.fa.", "dti.fa."),
+        ("perf.cbf.mean.", "cbf."),
+        (".jhu.icbm.labels.1mm", ""),
+        (".include.optic.radiation.", ""),
+        ("\.\.", "."),  # Replace double dots with single dot
+        ("\.\.", "."),  # Replace double dots with single dot
+        ("cerebellar.peduncle", "cereb.ped"),
+        (r"anterior.limb.of.internal.capsule", "ant.int.cap"),
+        (r"posterior.limb.of.internal.capsule", "post.int.cap"),
+        ("t1hier.", "t1."),
+        ("anterior", "ant"),
+        ("posterior", "post"),
+        ("inferior", "inf"),
+        ("superior", "sup"),
+        (r"dktcortex", ".ctx"),
+        (".lravg", ""),
+        ("dti.mean.fa", "dti.fa"),
+        (r"retrolenticular.part.of.internal", "rent.int.cap"),
+        (r"iculus.could.be.a.part.of.ant.internal.capsule", ""),  # Twice
+        (".fronto.occipital.", ".frnt.occ."),
+        (r".longitidinal.fasciculus.", ".long.fasc."),  # Twice
+        (".external.capsule", ".ext.cap"),
+        ("of.internal.capsule", ".int.cap"),
+        ("fornix.cres.stria.terminalis", "fornix."),
+        ("capsule", ""),
+        ("and.inf.frnt.occ.fasciculus.", ""),
+        ("crossing.tract.a.part.of.mcp.", "")
+      ]
+
+    # Apply substitutions in order
+    for pattern, replacement in substitutions:
+        if verbose:
+            print("Pre " + x + " pattern "+pattern + " repl " + replacement )
+        x = re.sub(pattern, replacement, x.lower(), flags=re.IGNORECASE)
+        if verbose:
+            print("Post " + x)
+
+    return x[:40]  # Truncate to first 40 characters
+
+
+def brainmap_figure(statistical_df, data_dictionary, output_prefix, brain_image, overlay_cmap='bwr', nslices=21, ncol=7, edge_image_dilation = 0, black_bg=True, axes = [0,1,2], fixed_overlay_range=None, crop=5, verbose=0 ):
     """
     Create figures based on statistical data and an underlying brain image.
 
@@ -10666,7 +10795,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
         with respect to regions that are measured in antspymm.   value will be 
         the value to be displayed.   if two examples of a given region exist in 
         statistical_df, then the largest absolute value will be taken for display.
-    - data_dictionary_path (str): Path to the data dictionary CSV file.
+    - data_dictionary (pandas dataframe): antspymm data dictionary.
     - output_prefix (str): Prefix for the output figure filenames.
     - brain_image (antsImage): the brain image on which results will overlay.
     - overlay_cmap (str): see matplotlib
@@ -10684,11 +10813,14 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
     """
     import re
 
+    def is_bst_region(filename):
+        return filename[-4:] == '.bst'
+
     # Read the statistical file
     zz = statistical_df 
     
     # Read the data dictionary from a CSV file
-    mydict = pd.read_csv(data_dictionary_path)
+    mydict = data_dictionary
     mydict = mydict[~mydict['Measurement'].str.contains("tractography-based connectivity", na=False)]
     mydict2=mydict.copy()
     mydict2['tidynames']=mydict2['tidynames'].str.replace(".left","")
@@ -10719,8 +10851,18 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             if verbose > 0 :
                 print(str(k) +  " " + anattoshow[k]  )
             mysub = zz[zz['anat'].str.contains(anattoshow[k])]
-            anatsear=re.sub(r'[()]', '.', anattoshow[k])
-            anatsear=re.sub(r'\.\.', '.', anatsear)
+            anatsear=shorten_pymm_names( anattoshow[k] )
+            anatsear=re.sub(r'[()]', '.', anatsear )
+            anatsear=re.sub(r'\.\.', '.', anatsear )
+            anatsear=re.sub("dti.mean.md.snc","md.snc",anatsear)
+            anatsear=re.sub("dti.mean.fa.snc","fa.snc",anatsear)
+            anatsear=re.sub("dti.mean.md.snr","md.snr",anatsear)
+            anatsear=re.sub("dti.mean.fa.snr","fa.snr",anatsear)
+            anatsear=re.sub("dti.mean.md.","",anatsear)
+            anatsear=re.sub("dti.mean.fa.","",anatsear)
+            anatsear=re.sub("dti.md.","",anatsear)
+            anatsear=re.sub("dti.fa.","",anatsear)
+            anatsear=re.sub("dti.md","",anatsear)
             anatsear=re.sub("dti.fa","",anatsear)
             anatsear=re.sub("cbf.","",anatsear)
             anatsear=re.sub("rsfmri.fcnxpro122.","",anatsear)
@@ -10741,12 +10883,6 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             anatsear=re.sub("t1.area.","",anatsear)
             anatsear=re.sub("asymdp.","",anatsear)
             anatsear=re.sub("asym.","",anatsear)
-            anatsear=re.sub("dti.md.","",anatsear)
-            anatsear=re.sub("dti.fa.","",anatsear)
-            anatsear=re.sub("dti.md","",anatsear)
-            anatsear=re.sub("dti.mean.md.","",anatsear)
-            anatsear=re.sub("dti.mean.fa.","",anatsear)
-            anatsear=re.sub("asym.","",anatsear)
             anatsear=re.sub("asym","",anatsear)
             anatsear=re.sub("lravg.","",anatsear)
             anatsear=re.sub("lravg","",anatsear)
@@ -10756,22 +10892,38 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             anatsear=re.sub("superior","sup",anatsear)
             anatsear=re.sub("cerebellum","",anatsear)
             anatsear=re.sub("brainstem","",anatsear)
+            anatsear=re.sub("t.limb.int","t.int",anatsear)
+            anatsear=re.sub("paracentral","paracent",anatsear)
+            anatsear=re.sub("precentral","precent",anatsear)
+            anatsear=re.sub("postcentral","postcent",anatsear)
             anatsear=re.sub("sup.cerebellar.peduncle","sup.cereb.ped",anatsear)
             anatsear=re.sub("inferior.cerebellar.peduncle","inf.cereb.ped",anatsear)
             anatsear=re.sub(".crossing.tract.a.part.of.mcp.","",anatsear)
+            anatsear=re.sub(".crossing.tract.a.part.of.","",anatsear)
             anatsear=re.sub(".column.and.body.of.fornix.","",anatsear)
-            anatsear=re.sub("fronto.occipital.fasciculus.could.be.a.part.of.anterior.internal.capsule","frnt.occ",anatsear)
+            anatsear=re.sub("fronto.occipital.fasciculus.could.be.a.part.of.ant.internal.capsule","frnt.occ",anatsear)
             anatsear=re.sub("inferior.fronto.occipital.fasciculus.could.be.a.part.of.anterior.internal.capsule","inf.frnt.occ",anatsear)
             anatsear=re.sub("fornix.cres.stria.terminalis.can.not.be.resolved.with.current.resolution","fornix.column.and.body.of.fornix",anatsear)
             anatsear=re.sub("external.capsule","ext.cap",anatsear)
             anatsear=re.sub(".jhu.icbm.labels.1mm","",anatsear)
+            anatsear=re.sub("dp.",".",anatsear)
+            anatsear=re.sub(".mtg.sn.snc.",".snc.",anatsear)
+            anatsear=re.sub(".mtg.sn.snr.",".snr.",anatsear)
             anatsear=re.sub("mtg.sn.snc.",".snc.",anatsear)
             anatsear=re.sub("mtg.sn.snr.",".snr.",anatsear)
+            anatsear=re.sub("mtg.sn.snc",".snc.",anatsear)
+            anatsear=re.sub("mtg.sn.snr",".snr.",anatsear)
             anatsear=re.sub("anterior.","ant.",anatsear)
+            anatsear=re.sub("rsf.","",anatsear)
+            anatsear=re.sub("fcnxpro122.","",anatsear)
+            anatsear=re.sub("fcnxpro129.","",anatsear)
+            anatsear=re.sub("fcnxpro134.","",anatsear)
             anatsear=re.sub("ant.corona.radiata","ant.cor.rad",anatsear)
             anatsear=re.sub("sup.corona.radiata","sup.cor.rad",anatsear)
             anatsear=re.sub("posterior.thalamic.radiation.include.optic.radiation","post.thalamic.radiation",anatsear)
             anatsear=re.sub("retrolenticular.part.of.internal.capsule","rent.int.cap",anatsear)
+            anatsear=re.sub("post.limb.of.internal.capsule","post.int.cap",anatsear)
+            anatsear=re.sub("ant.limb.of.internal.capsule","ant.int.cap",anatsear)
             anatsear=re.sub("sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus","ilf.and.ifo",anatsear)
             atlassearch = mydict['tidynames'].str.contains(anatsear)
             if atlassearch.sum() == 0:
@@ -10796,7 +10948,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
                 myext = 'JHU_wm'
             elif 'dktcortex' in anattoshow[k] or whichatlas == 'desikan-killiany-tourville' or 'dtkregions' in anattoshow[k]  :
                 myext = 'dkt_cortex'
-            elif ('cit168' in anattoshow[k] or whichatlas == 'CIT168') and not 'brainstem' in anattoshow[k]:
+            elif ('cit168' in anattoshow[k] or whichatlas == 'CIT168') and not 'brainstem' in anattoshow[k] and not is_bst_region(anatsear):
                 myext = 'cit168lab'
             elif 'mtl' in anattoshow[k]:
                 myext = 'mtl'
@@ -10805,7 +10957,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
                 myext = 'cerebellum'
                 oglabelname=re.sub('cerebellum', '',anatsear)
                 # oglabelname=oglabelname[2:]
-            elif 'brainstem' in anattoshow[k]:
+            elif 'brainstem' in anattoshow[k] or is_bst_region(anatsear):
                 myext = 'brainstem'
             elif any(item in anattoshow[k] for item in ['nbm', 'bf']):
                 myext = 'bf'

{antspymm-1.4.0.dist-info → antspymm-1.4.2.dist-info}/METADATA

@@ -1,18 +1,18 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.4.0
+Version: 1.4.2
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: h5py >=2.10.0
-Requires-Dist: numpy >=1.19.4
-Requires-Dist: pandas >=1.0.1
-Requires-Dist: antspyx >=0.4.2
-Requires-Dist: antspynet >=0.2.8
-Requires-Dist: antspyt1w >=0.9.3
+Requires-Dist: h5py>=2.10.0
+Requires-Dist: numpy>=1.19.4
+Requires-Dist: pandas>=1.0.1
+Requires-Dist: antspyx>=0.4.2
+Requires-Dist: antspynet>=0.2.8
+Requires-Dist: antspyt1w>=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
@@ -112,6 +112,66 @@ achieved through four steps (recommended approach):
 
 4. run the main antspymm function
 
+# formal description
+
+<details>
+<summary>Overview</summary>
+
+The Advanced Normalization Tools Ecosystem (ANTsX) is a collection of interrelated, open-source software libraries for biological and medical image processing [1](https://pubmed.ncbi.nlm.nih.gov/33907199/) and analysis built on the NIH’s Insight Toolkit (ITK).  ANTsX has demonstrated significant applicability for a variety of organ systems, species, and imaging modalities [2](https://pubmed.ncbi.nlm.nih.gov/25977810/) [3](https://pubmed.ncbi.nlm.nih.gov/38746199/) [4](https://pubmed.ncbi.nlm.nih.gov/35703369/).  ANTsX-based processing of multi-modality studies utilizes the Python-based ANTsPyMM library.  This includes structural (T1-w, DTI, FLAIR), functional (fMRI), and perfusion (ASL) modalities.
+
+</details>
+
+<details>
+<summary>T1-weighted MRI</summary>
+
+T1-weighted MRI processing has been previously described [1](https://pubmed.ncbi.nlm.nih.gov/33907199/) [2](https://pubmed.ncbi.nlm.nih.gov/38632390/).  It is coordinated by ANTsPyT1w, a sub-component of ANTsPyMM, and includes tools for image registration, segmentation, and super-resolution as customized for the human brain. Processing components include preprocessing (denoising + bias correction), brain extraction, sis-tissue parenchymal parcellation (CSF, gray matter, white matter, deep gray matter, brain stem, and cerebellum), and cortical parcellation for morphological quantitation.  Derived measurements are tabulated by the neuroanatomical coordinates defined above and include cortical and subcortical measurements and morphological measurements of the hippocampus, basal forebrain and cerebellum.
+
+</details>
+
+<details>
+<summary>Diffusion</summary>
+
+Diffusion processing.  ANTsPyMM couples the ANTsX toolkit with the Diffusion Imaging in Python (Dipy) library for the processing and analysis of diffusion MRI [1](https://pubmed.ncbi.nlm.nih.gov/24600385/).   The former is used for motion correction and normalization to corresponding T1-w images.  Output consists of QC images, the motion corrected diffusion series, RGB images, FA, mean diffusion and dense tractography as well as tractography-based connectivity matrices.  Tabular summary of these metrics are written to csv.
+
+</details>
+
+<details>
+<summary>Resting-state fMRI</summary>
+
+The rsfMRI processing computes a robust summary of resting-state fMRI time series data and corrects for motion artifacts, extracts temporal statistics, and computes functional connectivity across the brain. The analysis pipeline incorporates advanced techniques for noise reduction, temporal derivative calculation, signal standardization, and the calculation of functional connectivity between brain regions using Yeo homotopic labels. This provides researchers with cleaned, standardized, and biologically meaningful data for further analysis of brain network activity.
+
+Several preprocessing steps are included in the ANTsPyMM processing of resting state fMRI (rsfMRI) data.  First, motion correction is used to align the time series to a series specific fMRI template.  Distortion correction to t1 is also performed along with brain extraction.  The **temporal derivative** is calculated to quantify changes over time in the signal, followed by the **temporal standard deviation (tSTD)**, which computes the variability across time for each voxel. This is done to identify regions of interest with significant signal variation. The **CompCor matrix** [1](https://pubmed.ncbi.nlm.nih.gov/17560126/) is computed using temporal standard deviation thresholds, which helps remove noise by identifying high-variance regions. Additionally, **motion correction** is a central part of the pipeline, where metrics like framewise displacement (FD) and motion-induced signal changes (DVARS) are calculated to detect and correct for artifacts caused by subject movement. **Bandpass filtering** is applied to focus the analysis on brain signals within specific frequency ranges, and **censoring** is used to exclude high-motion time points from the analysis, ensuring cleaner data. The preprocessing concludes with the calculation of **summary statistics**, including measures of signal-to-noise ratio (SNR) and motion effects, which are compiled into a dictionary for further use.
+
+The next step in the pipeline involves computing functional connectivity through **correlation matrices** based on the **Yeo homotopic labels**, which group brain regions into homotopic (mirrored) areas across hemispheres. Time series data are averaged within each Yeo-labeled region, and pairwise **correlation matrices** are computed to assess the functional connectivity both within and between brain hemispheres. This allows for an in-depth analysis of large-scale brain networks, including symmetrical interactions between homotopic regions and connectivity within networks such as the default mode network, visual network, and others.
+
+This provides a comprehensive framework for preprocessing resting-state fMRI data and analyzing functional connectivity across the brain. By combining robust noise reduction, motion correction, and correlation matrix computation, the pipeline ensures that the resulting data are suitable for high-quality research into brain network dynamics and resting-state connectivity. Through the use of Yeo homotopic labels and functional correlation matrices, the code offers a valuable tool for investigating symmetrical brain activity and network interactions in fMRI studies. By default, three different sets of processing parameters are employed.  These were chosen based on an empirical evaluation of reproducibility in a traveling participant cohort.
+
+</details>
+
+<details>
+<summary>ASL</summary>
+
+ASL processing.  Cerebral blood flow (CBF) is a critical parameter in understanding brain function and its alterations in various neurological conditions. Arterial spin labeling (ASL) MRI is a non-invasive technique that can measure CBF without the need for contrast agents. ANTsPyMM estimates CBF from ASL MRI data through a combination of image processing and mathematical modeling techniques [1](https://pubmed.ncbi.nlm.nih.gov/24715426/).  First, motion artifacts and outliers are removed from the time series data.  Second, the preprocessed data is registered to the reference T1-w space using a rigid transformation optimized through the ANTs registration tools [2](https://pubmed.ncbi.nlm.nih.gov/24817849/).  Third, the six-tissue segmentation generated during the T1-w segmentation is used to partition the registered ASL data from which the CBF is estimated using a mathematical model that takes into account the ASL MRI signal, the labeling efficiency, and the longitudinal relaxation time of blood.  Finally, the M0 image, which represents the equilibrium magnetization of brain tissue, is estimated using a separate mathematical model.
+
+</details>
+
+<details>
+<summary>Magnetic resonance angiography</summary>
+
+MRA processing and analysis.   A precursor for quantitative measures of potential vascular irregularities is the segmentation derived from MR angiography.  To extract these image-based quantitative measures (described below), we developed and trained a deep learning network as part of the ANTsXNet functional library.  Training data was adapted from a publicly available resource [1](https://data.kitware.com/#item/58a372e48d777f0721a64dc9) consisting of 42 subjects with vascular network segmentations and brain masks provided.  A previously constructed high-resolution template was generated from the Human Connectome Project Young Adult cohort comprising T1-w, T2-w, and FA modalities using ANTs functionality [2](https://pubmed.ncbi.nlm.nih.gov/19818860/) [3](https://pubmed.ncbi.nlm.nih.gov/25433513/) and served as the prediction space for network training.  Prior spatial information was included by warping all vascular segmentations to the template space, averaged, spatially smoothed, and renormalized to the intensity range [0,1].  Aggressive data augmentation was used to generate additional data in real time during training consisting of random spatial linear and deformable transformations, random Gaussian additive noise, random histogram-based intensity warping [4](https://pubmed.ncbi.nlm.nih.gov/34227163/), and simulated bias field based on the popular N4 algorithm [5](https://pubmed.ncbi.nlm.nih.gov/20378467/). The functionality is available as open-source in both the R-based ANTsRNet (``brainMraVesselSegmentation(...)``) and Python-based ANTsPyNet (``brain_mra_vessel_segmentation(...)``).
+
+</details>
+
+<details>
+<summary>Periventricular spaces and white matter hyperintensities</summary>
+
+Traditional measures for indicating abnormal vascular morphology can then be calculated, such as tortuosity [1](https://pubmed.ncbi.nlm.nih.gov/12956271/).  For example, tight vascular coils (i.e., high tortuosity) are often associated with the presence of malignant tumors.  From the centerline of the vessel segmentation, various tortuosity measures have been proposed including 1) distance metric: the ratio of the length of the centerline to the distance between the two endpoints, 2) inflection count metric: the distance metric multiplied by the number of the inflection points (i.e., a point of minimum total curvature), 3) sum of angles metric: the integrated total curvature normalized by total path length.   
+
+For quantitative assessment of enlarged perivascular spaces, we employ functionality made publicly available through the ANTsX toolkit.  Specifically, previous published research [2](https://pubmed.ncbi.nlm.nih.gov/34262443/) has been ported to the ANTsXNet library and will be used for segmenting enlarged perivascular spaces.  Using both T1 and FLAIR modalities, a trained deep learning U-net neural network was trained using 40 datasets in which all visible perivascular spaces were manually annotated by an expert.  An ensemble of trained weights is used to produce the final probability image.  Previous work in MRI super resolution [3](https://www.medrxiv.org/content/10.1101/2023.02.02.23285376v1) will be used to explore the possible output enhancement.  PVS segmentation results will be tabulated per lobe using separate ANTsXNet functionality [4](https://pubmed.ncbi.nlm.nih.gov/38632390/).
+
+Similar functionality exists for segmentation of white matter hyperintensities and will be included in the MRI processing for this project.  Several algorithms have been ported to ANTsXNet from previous research from multiple groups to complement existing capabilities [5](https://pubmed.ncbi.nlm.nih.gov/30125711/) [6](https://pubmed.ncbi.nlm.nih.gov/35088930/) [7](https://pubmed.ncbi.nlm.nih.gov/38050769/).  Regional tabulation will also depend on the lobar segmentation within the white matter as with the PVS segmentation results.
+
+</details>
 
 # first time setup
 

antspymm-1.4.2.dist-info/RECORD

@@ -0,0 +1,7 @@
+antspymm/__init__.py,sha256=qUzRd3GmYB8hSO7GNaBuP7Jlm0QNMttTaUfvIpeeAig,4497
+antspymm/mm.py,sha256=iZvIpNvltqqzmtEF1D9tDoMUIbJK-GpsOjzSaH3z1ns,503059
+antspymm-1.4.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+antspymm-1.4.2.dist-info/METADATA,sha256=6Z-7BaP2_duk8af-kmSXg99BZcCzbWm7yhsxvxi7JRk,25668
+antspymm-1.4.2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+antspymm-1.4.2.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.4.2.dist-info/RECORD,,

{antspymm-1.4.0.dist-info → antspymm-1.4.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.3.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

antspymm-1.4.0.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
-antspymm/mm.py,sha256=mSizSFmJEisEuzVdBozOxKwg7GtxPPT299q6vOmOII0,495807
-antspymm-1.4.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.4.0.dist-info/METADATA,sha256=SXTcovYb7YSYn1K7xHKhwq9fE2QpJxGVfVv63VBFwk8,14866
-antspymm-1.4.0.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
-antspymm-1.4.0.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.4.0.dist-info/RECORD,,