antspymm 1.4.1__py3-none-any.whl → 1.4.3__py3-none-any.whl

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=24, target_extension='.csv' ):
+def get_data( name=None, force_download=False, version=25, target_extension='.csv' ):
     """
     Get ANTsPyMM data filename
 
@@ -2738,11 +2738,47 @@ def get_data( name=None, force_download=False, version=24, target_extension='.cs
     """
     os.makedirs(DATA_PATH, exist_ok=True)
 
+    def mv_subfolder_files(folder, verbose=False):
+        """
+        Move files from subfolders to the parent folder.
+
+        Parameters
+        ----------
+        folder : str
+            Path to the folder.
+        verbose : bool, optional
+            Print information about the files and folders being processed (default is False).
+
+        Returns
+        -------
+        None
+        """
+        import os
+        import shutil
+        for root, dirs, files in os.walk(folder):
+            if verbose:
+                print(f"Processing directory: {root}")
+                print(f"Subdirectories: {dirs}")
+                print(f"Files: {files}")
+            
+            for file in files:
+                if root != folder:
+                    if verbose:
+                        print(f"Moving file: {file} from {root} to {folder}")
+                    shutil.move(os.path.join(root, file), folder)
+            
+            for dir in dirs:
+                if root != folder:
+                    if verbose:
+                        print(f"Removing directory: {dir} from {root}")
+                    shutil.rmtree(os.path.join(root, dir))
+
     def download_data( version ):
         url = "https://figshare.com/ndownloader/articles/16912366/versions/" + str(version)
         target_file_name = "16912366.zip"
         target_file_name_path = tf.keras.utils.get_file(target_file_name, url,
             cache_subdir=DATA_PATH, extract = True )
+        mv_subfolder_files( os.path.expanduser("~/.antspymm"), False )
         os.remove( DATA_PATH + target_file_name )
 
     if force_download:
@@ -2762,6 +2798,7 @@ def get_data( name=None, force_download=False, version=24, target_extension='.cs
                 fname = os.path.join(DATA_PATH, fname)
                 files.append(fname)
 
+
     if name == 'all':
         return files
 
@@ -10899,6 +10936,7 @@ def brainmap_figure(statistical_df, data_dictionary, output_prefix, brain_image,
             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.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)
@@ -10914,6 +10952,9 @@ def brainmap_figure(statistical_df, data_dictionary, output_prefix, brain_image,
             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)

{antspymm-1.4.1.dist-info → antspymm-1.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.4.1
+Version: 1.4.3
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0
@@ -138,7 +138,13 @@ Diffusion processing.  ANTsPyMM couples the ANTsX toolkit with the Diffusion Ima
 <details>
 <summary>Resting-state fMRI</summary>
 
-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.  A homotopic coordinate system is transformed to the time series space and used to derive network correlation matrices.  CompCor is used to model physiological noise [1](https://pubmed.ncbi.nlm.nih.gov/17560126/).  Censoring is performed for problematic volumes.  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.  Several QC measurements are derived and all of these data are summarized in a tabular format.
+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>
 

antspymm-1.4.3.dist-info/RECORD

@@ -0,0 +1,7 @@
+antspymm/__init__.py,sha256=qUzRd3GmYB8hSO7GNaBuP7Jlm0QNMttTaUfvIpeeAig,4497
+antspymm/mm.py,sha256=2X6zZaERE8tPbzkcyNGD8vIZcpA1T3ej24_jGOnESRA,504283
+antspymm-1.4.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+antspymm-1.4.3.dist-info/METADATA,sha256=YSSsqoF26p_IVPzEtiShVaNwBc5Bue3FPfZY6iVaCnY,25668
+antspymm-1.4.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+antspymm-1.4.3.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.4.3.dist-info/RECORD,,

{antspymm-1.4.1.dist-info → antspymm-1.4.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

antspymm-1.4.1.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=qUzRd3GmYB8hSO7GNaBuP7Jlm0QNMttTaUfvIpeeAig,4497
-antspymm/mm.py,sha256=9UZz8Q71VcA92kIBI3odttbbaePJMnJTn1cp7uVeig4,502824
-antspymm-1.4.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.4.1.dist-info/METADATA,sha256=Bs0pXkMaoVJZlIMJDnm9eqMFtGwCu9ziFZ5ZKaQ0p2Y,23118
-antspymm-1.4.1.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-antspymm-1.4.1.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.4.1.dist-info/RECORD,,