antspymm 1.2.7__tar.gz → 1.3.1__tar.gz

{antspymm-1.2.7/antspymm.egg-info → antspymm-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.2.7
+Version: 1.3.1
 Summary: multi-channel/time-series medical image processing with antspyx
 Home-page: https://github.com/stnava/ANTsPyMM
 Author: Avants, Gosselin, Tustison, Reardon
@@ -22,8 +22,7 @@ Requires-Dist: scikit-learn
 
 # ANTsPyMM
 
-
-[mapping](https://imgur.com/a/XzpXI3i)
+![mapping](https://i.imgur.com/qKqYjU9.jpeg)
 
 ## processing utilities for timeseries/multichannel images - mostly neuroimaging
 
@@ -57,16 +56,18 @@ ANTsPyMM will process several types of brain MRI into tabular form as well as no
 
     * basal forebrain (Avants et al HBM 2022 abstract)
 
-    * other regions (egMTL) 10.1101/2023.01.17.23284693
+    * other regions (eg MTL) 10.1101/2023.01.17.23284693
 
     * also produces jacobian data
 
 * rsfMRI: resting state functional MRI
 
-    * uses 10.1016/j.conb.2012.12.009 to estimate network specific correlations
+    * uses [a recent homotopic parcellation](https://pubmed.ncbi.nlm.nih.gov/36918136/) to estimate network specific correlations
 
     * f/ALFF 10.1016/j.jneumeth.2008.04.012
 
+    * [percent absolute fluctuation](https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.888174/full)
+
 * NM2DMT: neuromelanin mid-brain images
 
     * CIT168 template 10.1101/211201
@@ -124,6 +125,8 @@ package data is installed.
 
 NOTE: some functions in `antspynet` will download deep network model weights on the fly.  if one is containerizing, then it would be worth running a test case through in the container to make sure all the relevant weights are pre-downloaded.
 
+NOTE: an example process for BIDS data on a cluster is [here](https://github.com/stnava/ANTPD_antspymm).  this repo is also a good place to try to learn how to use this tool.
+
 # example processing
 
 see the latest help but this snippet gives an idea of how one might use the package:
@@ -205,7 +208,7 @@ matched_mm_data2.to_csv( "matched_mm_data2.csv", index=False )
 
 ## an example on open neuro (BIDS) data
 
-from : [ANT PD](https://openneuro.org/datasets/ds001907/versions/3.0.2)
+from : [ANT PD](https://openneuro.org/datasets/ds001907/versions/3.0.2)   see also [this repo](https://github.com/stnava/ANTPD_antspymm).
 
 ```
 imagesBIDS/

{antspymm-1.2.7 → antspymm-1.3.1}/README.md

@@ -1,7 +1,6 @@
 # ANTsPyMM
 
-
-[mapping](https://imgur.com/a/XzpXI3i)
+![mapping](https://i.imgur.com/qKqYjU9.jpeg)
 
 ## processing utilities for timeseries/multichannel images - mostly neuroimaging
 
@@ -35,16 +34,18 @@ ANTsPyMM will process several types of brain MRI into tabular form as well as no
 
     * basal forebrain (Avants et al HBM 2022 abstract)
 
-    * other regions (egMTL) 10.1101/2023.01.17.23284693
+    * other regions (eg MTL) 10.1101/2023.01.17.23284693
 
     * also produces jacobian data
 
 * rsfMRI: resting state functional MRI
 
-    * uses 10.1016/j.conb.2012.12.009 to estimate network specific correlations
+    * uses [a recent homotopic parcellation](https://pubmed.ncbi.nlm.nih.gov/36918136/) to estimate network specific correlations
 
     * f/ALFF 10.1016/j.jneumeth.2008.04.012
 
+    * [percent absolute fluctuation](https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.888174/full)
+
 * NM2DMT: neuromelanin mid-brain images
 
     * CIT168 template 10.1101/211201
@@ -102,6 +103,8 @@ package data is installed.
 
 NOTE: some functions in `antspynet` will download deep network model weights on the fly.  if one is containerizing, then it would be worth running a test case through in the container to make sure all the relevant weights are pre-downloaded.
 
+NOTE: an example process for BIDS data on a cluster is [here](https://github.com/stnava/ANTPD_antspymm).  this repo is also a good place to try to learn how to use this tool.
+
 # example processing
 
 see the latest help but this snippet gives an idea of how one might use the package:
@@ -183,7 +186,7 @@ matched_mm_data2.to_csv( "matched_mm_data2.csv", index=False )
 
 ## an example on open neuro (BIDS) data
 
-from : [ANT PD](https://openneuro.org/datasets/ds001907/versions/3.0.2)
+from : [ANT PD](https://openneuro.org/datasets/ds001907/versions/3.0.2)   see also [this repo](https://github.com/stnava/ANTPD_antspymm).
 
 ```
 imagesBIDS/

{antspymm-1.2.7 → antspymm-1.3.1}/antspymm/__init__.py

@@ -81,6 +81,7 @@ from .mm import version
 from .mm import best_mmm
 from .mm import nrg_2_bids
 from .mm import bids_2_nrg
+from .mm import validate_nrg_file_format
 from .mm import parse_nrg_filename
 from .mm import novelty_detection_ee
 from .mm import novelty_detection_svm
@@ -122,4 +123,12 @@ from .mm import clean_tmp_directory
 from .mm import dict_to_dataframe
 from .mm import PerAF
 from .mm import get_antsimage_keys
+from .mm import filter_columns_by_nan_percentage
+from .mm import nrg_filename_to_subjectvisit
+from .mm import add_repeat_column
+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
+