diff --git a/docs/about.rst b/docs/about.rst index 713b8db99..b90b49647 100644 --- a/docs/about.rst +++ b/docs/about.rst @@ -43,11 +43,13 @@ or are never even translated from the original papers into useable tools. NiMARE operates on NIMADS-format datasets, which users will be able to compile by searching the NeuroStore database with the pyNIMADS library. A number of other services in the ecosystem will then use NiMARE functions to perform meta-analyses, including Neurosynth 2.0 and `NeuroVault`_. + Other Meta-Analytic Tools ------------------------- Outside of the shared ecosystem detailed above, there are a number of tools. + Coordinate-based meta-analysis tools ```````````````````````````````````` @@ -60,11 +62,13 @@ The `SDM`_ Toolbox: This toolbox contains the hybrid coordinate/image-based seed `NeuRoi Toolbox`_: This toolbox contains an implementation of the `Analysis of Brain Coordinates`_ (ABC) CBMA algorithm. + Image-based meta-analysis tools ``````````````````````````````` `IBMA SPM extension`_: This SPM extension implements a number of image-based meta-analysis algorithms. + Meta-analysis tools for other neuroimaging modalities ````````````````````````````````````````````````````` diff --git a/docs/conf.py b/docs/conf.py index f755d1c8d..e56c5619c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -174,7 +174,7 @@ "matplotlib": ("https://matplotlib.org/", (None, "https://matplotlib.org/objects.inv")), "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None), "nibabel": ("https://nipy.org/nibabel/", None), - "nilearn": ("http://nilearn.github.io/", None), + "nilearn": ("http://nilearn.github.io/stable/", None), "pymare": ("https://pymare.readthedocs.io/en/latest/", None), "skimage": ("https://scikit-image.org/docs/stable/", None), } diff --git a/docs/guide/annotation.rst b/docs/guide/annotation.rst new file mode 100644 index 000000000..9a212f6ab --- /dev/null +++ b/docs/guide/annotation.rst @@ -0,0 +1,15 @@ +Annotating Meta-Analytic Data +============================== + +Downloading abstracts for papers +-------------------------------- + +Extracting features from text +----------------------------- + +Annotating Datasets +------------------- + +References +---------- +.. footbibliography:: diff --git a/docs/guide/cbma.rst b/docs/guide/cbma.rst new file mode 100644 index 000000000..fd82d9a9e --- /dev/null +++ b/docs/guide/cbma.rst @@ -0,0 +1,107 @@ +Coordinate-Based Meta-Analysis +============================== + +Coordinate-based meta-analysis (CBMA) is a popular tool for measuring consistency across neuroimaging studies. +While :ref:`ibma` techniques leverage more information than CBMA, and are thus superior, +CBMA is much more popular because the majority of fMRI papers report peaks from significant clusters in tables, +rather than uploading unthresholded statistical maps to a database, like NeuroVault. + +.. note:: + This page walks through coordinate-based meta-analysis (CBMA) in NiMARE from a practical perspective. + The focus is on performing basic CBMAs. + For a more detailed description of the classes and functions used for CBMA, see + :ref:`sphx_glr_auto_examples_02_meta-analyses_03_plot_kernel_transformers.py`, + :ref:`sphx_glr_auto_examples_02_meta-analyses_01_plot_cbma.py`, and + :ref:`sphx_glr_auto_examples_02_meta-analyses_05_plot_correctors.py`. + +Types of CBMA studies +--------------------- +1. One large dataset, with multiple subsets. + + 1. Create a single, large Dataset with annotations indicating the subsets. + 2. Perform a meta-analysis on the full Dataset. + + - This omnibus analysis is typically interpreted as evaluating convergent results across the subsets. + + 3. Slice the Dataset into different subsets. + 4. Perform a meta-analysis on each subset. + 5. Perform a subtraction analysis between each subset and the rest of the subsets (combined in one Dataset). + 6. Perform functional decoding comparing something and something. + 7. Plot significant results. + +2. A direct comparison between two datasets. + + .. note:: + One conundrum meta-analysts often face is that papers may report a mixture of + within-group analyses and between-group analyses. + For example, if you are planning to perform a meta-analysis of the n-back task with the + comparison between 3-back and 1-back conditions, + you will likely find many papers that report both 3-back > control and 1-back > control results, + as well as many papers that only report 3-back > 1-back results. + + In the case of the former, the standard approach is to perform a subtraction analysis. + In the latter case, you would perform a single univariate meta-analysis. + Unfortunately, you cannot combine the two sets of results. + + 1. Create two Dataset objects. + 2. Perform a meta-analysis on each Dataset. + 3. Perform a subtraction analysis comparing the two Datasets. + 4. Perform a conjunction analysis assessing convergence between the two meta-analyses. + 5. Run :class:`~nimare.diagnostics.FocusCounter` or :class:`~nimare.diagnostics.Jackknife` on all meta-analysis results. + 6. Run :func:`~nilearn.reporting.get_clusters_table` on all meta-analysis results. + 7. Plot significant results. + +3. Large-scale analyses on a database. + + 1. Download Neurosynth or NeuroQuery. + 2. ... + 3. Plot significant results. + +Selecting studies for a meta-analysis +------------------------------------- + +Organizing the dataset in NiMARE +-------------------------------- +NiMARE contains several functions for converting common formats to Dataset objects. + +Performing the meta-analysis +---------------------------- + +.. literalinclude:: ../../examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py + :start-at: from nimare.meta.cbma import ALE + :end-at: knowledge_results = ale.fit(knowledge_dset) + +.. figure:: ../auto_examples/02_meta-analyses/images/sphx_glr_08_plot_cbma_subtraction_conjunction_001.png + :target: ../auto_examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.html + :align: center + :scale: 100 + +Multiple comparisons correction +------------------------------- + +.. literalinclude:: ../../examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py + :start-at: from nimare.correct import FWECorrector + :end-at: knowledge_corrected_results = corr.transform(knowledge_results) + +.. figure:: ../auto_examples/02_meta-analyses/images/sphx_glr_08_plot_cbma_subtraction_conjunction_002.png + :target: ../auto_examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.html + :align: center + :scale: 100 + +Saving the results +------------------ + +.. literalinclude:: ../../examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py + :start-at: knowledge_corrected_results.save_maps( + :end-at: ) + +Performing additional followup analyses +--------------------------------------- + +.. literalinclude:: ../../examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py + :start-at: from nimare.diagnostics import Jackknife + :end-at: knowledge_jackknife_table + +References +---------- +.. footbibliography:: diff --git a/docs/guide/data.rst b/docs/guide/data.rst new file mode 100644 index 000000000..4ee5de441 --- /dev/null +++ b/docs/guide/data.rst @@ -0,0 +1,24 @@ +Working with Meta-Analytic Data +=============================== + +The Neuroimaging Meta-Analysis Data Standard (NIMADS) +----------------------------------------------------- + +Downloading large databases +--------------------------- + +Converting datasets from BrainMap +--------------------------------- + +The Dataset object +------------------ + +:ref:`sphx_glr_auto_examples_01_datasets_01_plot_dataset_io.py` + +.. literalinclude:: ../../examples/01_datasets/01_plot_dataset_io.py + :start-after: # Now we can load and save the Dataset object + :end-before: os.remove("pain_dset.pkl") # cleanup + +References +---------- +.. footbibliography:: diff --git a/docs/guide/decoding.rst b/docs/guide/decoding.rst new file mode 100644 index 000000000..76d22a528 --- /dev/null +++ b/docs/guide/decoding.rst @@ -0,0 +1,18 @@ +Meta-Analytic Functional Decoding +================================= + +Decoding ROIs +------------- + +Decoding VOIs +------------- + +Decoding based on arbitrary subsets of the Dataset +-------------------------------------------------- + +Decoding statistical maps +------------------------- + +References +---------- +.. footbibliography:: diff --git a/docs/guide/ibma.rst b/docs/guide/ibma.rst new file mode 100644 index 000000000..9a27cbe38 --- /dev/null +++ b/docs/guide/ibma.rst @@ -0,0 +1,31 @@ +Image-Based Meta-Analysis +============================== + +Types of IBMA studies +--------------------- +1. A manually-curated set of statistical maps. + 1. Perform image-based meta-analysis. The choice of algorithm depends on the data available. + 2. Plot significant results. + 3. Characterize results in a table. + +Selecting studies for a meta-analysis +------------------------------------- + +Organizing the dataset in NiMARE +-------------------------------- + +Performing the meta-analysis +---------------------------- + +Multiple comparisons correction +------------------------------- + +Saving the results +------------------ + +Performing additional followup analyses +--------------------------------------- + +References +---------- +.. footbibliography:: diff --git a/docs/guide/introduction.rst b/docs/guide/introduction.rst new file mode 100644 index 000000000..71dbf449c --- /dev/null +++ b/docs/guide/introduction.rst @@ -0,0 +1,23 @@ +.. include:: ../links.rst + +Introduction to NiMARE +===================================== + +Meta-Analysis and Analyses Using Meta-Analytic Data +--------------------------------------------------- + +Getting Help +------------ + +If you have usage-related questions, please create a new topic on `NeuroStars `_ +with the `"nimare" tag `_. +The ``NiMARE`` developers follow NeuroStars, and will be able to answer your question there. + +If you have identified a bug in NiMARE, or would like to request a new feature or change, +you can `open an issue `_ on GitHub. +Please look through `open issues `_ before opening a new one, +to ensure that you are not duplicating an existing issue. + +References +---------- +.. footbibliography:: diff --git a/docs/guide/toc.rst b/docs/guide/toc.rst new file mode 100644 index 000000000..3ad151bfd --- /dev/null +++ b/docs/guide/toc.rst @@ -0,0 +1,12 @@ +User Guide +========== + +.. toctree:: + :numbered: + + introduction.rst + data.rst + cbma.rst + ibma.rst + annotation.rst + decoding.rst diff --git a/docs/index.rst b/docs/index.rst index 71caa82de..6fbd3c81d 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -122,15 +122,16 @@ Then, to cite NiMARE in your manuscript, we recommend something like the followi about installation + guide/toc api auto_examples/index - contributing - dev_guide cli outputs methods changelog glossary + contributing + dev_guide Indices and tables ------------------ diff --git a/docs/references.bib b/docs/references.bib index c7f681f96..80a255a92 100644 --- a/docs/references.bib +++ b/docs/references.bib @@ -221,6 +221,18 @@ @article{langner2014meta doi={10.1016/j.neuroimage.2014.06.007} } +@article{muller2018ten, + title={Ten simple rules for neuroimaging meta-analysis}, + author={M{\"u}ller, Veronika I and Cieslik, Edna C and Laird, Angela R and Fox, Peter T and Radua, Joaquim and Mataix-Cols, David and Tench, Christopher R and Yarkoni, Tal and Nichols, Thomas E and Turkeltaub, Peter E and others}, + journal={Neuroscience \& Biobehavioral Reviews}, + volume={84}, + pages={151--161}, + year={2018}, + publisher={Elsevier}, + doi={10.1016/j.neubiorev.2017.11.012}, + url={https://doi.org/10.1016/j.neubiorev.2017.11.012} +} + @article{newman2009distributed, title={Distributed algorithms for topic models.}, author={Newman, David and Asuncion, Arthur and Smyth, Padhraic and Welling, Max}, @@ -292,6 +304,19 @@ @article{Salo2022 journal = {NeuroLibre} } +@article{samartsidis2017coordinate, + title={The coordinate-based meta-analysis of neuroimaging data}, + author={Samartsidis, Pantelis and Montagna, Silvia and Nichols, Thomas E and Johnson, Timothy D}, + journal={Statistical science: a review journal of the Institute of Mathematical Statistics}, + volume={32}, + number={4}, + pages={580}, + year={2017}, + publisher={NIH Public Access}, + doi={10.1214/17-STS624}, + url={https://doi.org/10.1214/17-STS624} +} + @article{shaffer1995multiple, title={Multiple hypothesis testing}, author={Shaffer, Juliet Popper}, diff --git a/examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py b/examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py index 483f7652e..e1581d17c 100644 --- a/examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py +++ b/examples/02_meta-analyses/08_plot_cbma_subtraction_conjunction.py @@ -19,10 +19,6 @@ 5. Compare the two samples with a subtraction analysis. 6. Compare the two within-sample meta-analyses with a conjunction analysis. """ -import os - -import matplotlib.pyplot as plt -from nilearn.plotting import plot_stat_map ############################################################################### # Load Sleuth text files into Datasets @@ -33,33 +29,78 @@ # (e.g., correctly naming an object after hearing its auditory description) # while a second group of studies asked children to decide if two (or more) # words were semantically related to one another or not. +import os + from nimare.io import convert_sleuth_to_dataset from nimare.utils import get_resource_path -knowledge_file = os.path.join(get_resource_path(), "semantic_knowledge_children.txt") -related_file = os.path.join(get_resource_path(), "semantic_relatedness_children.txt") +knowledge_file = os.path.join(get_resource_path(), "Enge2021_knowledge.txt") +related_file = os.path.join(get_resource_path(), "Enge2021_relatedness.txt") +# Some papers reported MNI coordinates +objects_file_mni = os.path.join(get_resource_path(), "Enge2021_objects_mni.txt") +# Other papers reported Talairach coordinates +objects_file_talairach = os.path.join(get_resource_path(), "Enge2021_objects_talairach.txt") knowledge_dset = convert_sleuth_to_dataset(knowledge_file) related_dset = convert_sleuth_to_dataset(related_file) +objects_dset = convert_sleuth_to_dataset( + [ + objects_file_mni, + objects_file_talairach, # NiMARE will automatically convert the Talairach foci to MNI + ] +) ############################################################################### -# Individual group ALEs +# View the contents of one of the Sleuth files +with open(knowledge_file, "r") as fo: + sleuth_file_contents = fo.readlines() + +sleuth_file_contents = sleuth_file_contents[:20] +print("".join(sleuth_file_contents)) + +############################################################################### +# Meta-analysis of semantic knowledge experiments # ----------------------------------------------------------------------------- -# Computing separate ALE analyses for each group is not strictly necessary for -# performing the subtraction analysis but will help the experimenter to appreciate the -# similarities and differences between the groups. -from nimare.correct import FWECorrector from nimare.meta.cbma import ALE ale = ALE(null_method="approximate") knowledge_results = ale.fit(knowledge_dset) -related_results = ale.fit(related_dset) + +############################################################################### +# Plot the uncorrected statistical map +# ````````````````````````````````````````````````````````````````````````````` +from nilearn.plotting import plot_stat_map + +plot_stat_map( + knowledge_results.get_map("z"), + cut_coords=4, + display_mode="z", + title="Semantic knowledge", + threshold=2.326, # cluster-level p < .01, one-tailed + cmap="RdBu_r", + vmax=4, +) + +############################################################################### +# This z-statistic map is not corrected for multiple comparisons. +# In order to account for the many voxel-wise tests that are performed in +# parallel, we must apply some type of multiple comparisons correction. +# To that end, we will use an :class:`~nimare.correct.FWECorrector` with the +# Monte Carlo method. +# +# Multiple comparisons correction with a Monte Carlo procedure +# ----------------------------------------------------------------------------- +# We will use the cluster-level corrected map, using a cluster-defining +# threshold of p < 0.001 and 100 iterations. +# In the actual paper, :footcite:`enge2021meta` used 10000 iterations instead. +from nimare.correct import FWECorrector corr = FWECorrector(method="montecarlo", voxel_thresh=0.001, n_iters=100, n_cores=2) knowledge_corrected_results = corr.transform(knowledge_results) -related_corrected_results = corr.transform(related_results) -fig, axes = plt.subplots(figsize=(12, 10), nrows=2) +############################################################################### +# Plot the corrected statistical map +# ````````````````````````````````````````````````````````````````````````````` knowledge_img = knowledge_corrected_results.get_map( "z_desc-size_level-cluster_corr-FWE_method-montecarlo" ) @@ -71,10 +112,45 @@ threshold=2.326, # cluster-level p < .01, one-tailed cmap="RdBu_r", vmax=4, - axes=axes[0], - figure=fig, ) +############################################################################### +# Save the results to disk +# ````````````````````````````````````````````````````````````````````````````` +knowledge_corrected_results.save_maps( + output_dir=".", + prefix="Enge2021_knowledge", +) + +############################################################################### +# Characterize the relative contributions of experiments in the results +# ````````````````````````````````````````````````````````````````````````````` +# NiMARE contains two methods for this: :class:`~nimare.diagnostics.Jackknife` +# and :class:`~nimare.diagnostics.FocusCounter`. +# We will show both below, but for the sake of speed we will only apply one to +# each subgroup meta-analysis. +from nimare.diagnostics import Jackknife + +jackknife = Jackknife( + target_image="z_desc-size_level-cluster_corr-FWE_method-montecarlo", + voxel_thresh=None, +) +knowledge_jackknife_table, _ = jackknife.transform(knowledge_corrected_results) +knowledge_jackknife_table + +############################################################################### +# Meta-analysis of semantic relatedness experiments +# ----------------------------------------------------------------------------- +ale = ALE(null_method="approximate") +related_results = ale.fit(related_dset) + +# Perform Monte Carlo-based multiple comparisons correction +corr = FWECorrector(method="montecarlo", voxel_thresh=0.001, n_iters=100, n_cores=2) +related_corrected_results = corr.transform(related_results) + +############################################################################### +# Plot the resulting statistical map +# ````````````````````````````````````````````````````````````````````````````` related_img = related_corrected_results.get_map( "z_desc-size_level-cluster_corr-FWE_method-montecarlo" ) @@ -86,59 +162,91 @@ threshold=2.326, # cluster-level p < .01, one-tailed cmap="RdBu_r", vmax=4, - axes=axes[1], - figure=fig, ) -fig.show() ############################################################################### -# Characterize the relative contributions of experiments in the ALE results -# ----------------------------------------------------------------------------- -# NiMARE contains two methods for this: :class:`~nimare.diagnostics.Jackknife` -# and :class:`~nimare.diagnostics.FocusCounter`. -# We will show both below, but for the sake of speed we will only apply one to -# each subgroup meta-analysis. -from nimare.diagnostics import FocusCounter - -counter = FocusCounter( +# Characterize the relative contributions of experiments in the results +# ````````````````````````````````````````````````````````````````````````````` +jackknife = Jackknife( target_image="z_desc-size_level-cluster_corr-FWE_method-montecarlo", voxel_thresh=None, ) -knowledge_count_table, _ = counter.transform(knowledge_corrected_results) -knowledge_count_table.head(10) +related_jackknife_table, _ = jackknife.transform(related_corrected_results) +related_jackknife_table ############################################################################### -from nimare.diagnostics import Jackknife +# Meta-analysis of semantic object experiments +# ----------------------------------------------------------------------------- +ale = ALE(null_method="approximate") +objects_results = ale.fit(objects_dset) + +# Perform Monte Carlo-based multiple comparisons correction +corr = FWECorrector(method="montecarlo", voxel_thresh=0.001, n_iters=100, n_cores=2) +objects_corrected_results = corr.transform(objects_results) + +############################################################################### +# Plot the resulting statistical map +# ````````````````````````````````````````````````````````````````````````````` +objects_img = objects_corrected_results.get_map( + "z_desc-size_level-cluster_corr-FWE_method-montecarlo" +) +plot_stat_map( + objects_img, + cut_coords=4, + display_mode="z", + title="Semantic objects", + threshold=2.326, # cluster-level p < .01, one-tailed + cmap="RdBu_r", + vmax=4, +) +############################################################################### +# Characterize the relative contributions of experiments in the results +# ````````````````````````````````````````````````````````````````````````````` jackknife = Jackknife( target_image="z_desc-size_level-cluster_corr-FWE_method-montecarlo", voxel_thresh=None, ) -related_jackknife_table, _ = jackknife.transform(related_corrected_results) -related_jackknife_table.head(10) +objects_jackknife_table, _ = jackknife.transform(objects_corrected_results) +objects_jackknife_table ############################################################################### -# Subtraction analysis +# Compare semantic knowledge to the other conditions with subtraction analysis # ----------------------------------------------------------------------------- -# Typically, one would use at least 10000 iterations for a subtraction analysis. -# However, we have reduced this to 100 iterations for this example. +# The semantic knowledge experiments can be compared to the experiments from +# the other two conditions by first merging the other two sets of experiments +# into a single Dataset, and then performing a subtraction analysis between the +# semantic knowledge Dataset and the new semantic relatedness/objects Dataset. +# +# In :footcite:t:`enge2021meta`, additional subtraction analyses were performed +# for semantic relatedness vs. (knowledge + objects) and semantic objects vs. +# (knowledge + relatedness). +# However, for the sake of executing this example online, we only perform the +# first of these analyses. +# +# .. important:: +# Typically, one would use at least 10000 iterations for a subtraction analysis. +# However, we have reduced this to 100 iterations for this example. from nimare.meta.cbma import ALESubtraction +# First, we combine the relatedness and objects Datasets +related_and_objects_dset = related_dset.merge(objects_dset) + sub = ALESubtraction(n_iters=100, n_cores=1) -res_sub = sub.fit(knowledge_dset, related_dset) +res_sub = sub.fit(knowledge_dset, related_and_objects_dset) img_sub = res_sub.get_map("z_desc-group1MinusGroup2") plot_stat_map( img_sub, cut_coords=4, display_mode="z", - title="Subtraction", + title="Knowledge > Other", cmap="RdBu_r", vmax=4, ) ############################################################################### -# Conjunction analysis +# Evaluate convergence across datasets with a conjunction analysis # ----------------------------------------------------------------------------- # To determine the overlap of the meta-analytic results, a conjunction image # can be computed by (a) identifying voxels that were statistically significant @@ -149,8 +257,12 @@ # :func:`nilearn.image.math_img`. from nilearn.image import math_img -formula = "np.where(img1 * img2 > 0, np.minimum(img1, img2), 0)" -img_conj = math_img(formula, img1=knowledge_img, img2=related_img) +img_conj = math_img( + "np.where((img1 * img2 * img3) > 0, np.minimum(img1, np.minimum(img2, img3)), 0)", + img1=knowledge_img, + img2=related_img, + img3=objects_img, +) plot_stat_map( img_conj, diff --git a/nimare/resources/semantic_knowledge_children.txt b/nimare/resources/Enge2021_knowledge.txt similarity index 100% rename from nimare/resources/semantic_knowledge_children.txt rename to nimare/resources/Enge2021_knowledge.txt diff --git a/nimare/resources/Enge2021_objects_mni.txt b/nimare/resources/Enge2021_objects_mni.txt new file mode 100644 index 000000000..51e09ac26 --- /dev/null +++ b/nimare/resources/Enge2021_objects_mni.txt @@ -0,0 +1,85 @@ +// Reference=MNI +// dekker2014pw: 9-10 year olds +// Subjects=10 +-28 -82 14 +50 -60 -8 +24 -68 56 +-48 -64 -12 +-38 26 18 +-26 -52 -14 +-44 6 28 +18 -94 8 +46 -76 -2 +-20 -88 10 + +// dekker2014pw: 7-8 year olds +// Subjects=11 +-36 -52 52 +30 -78 16 +-48 -64 -8 +52 -60 -18 +-50 6 26 +-24 -12 50 +18 -94 6 + +// liebig2017nd +// Subjects=41 +26 -96 -4 +38 -92 -6 +-27 -98 -8 +-33 -90 -8 +-42 -52 -18 +-51 -38 6 +-30 -62 42 +-39 6 30 +-51 30 18 +-51 22 28 +-4 20 52 +33 22 -4 +36 32 -6 +9 -82 -26 +-8 -81 -27 + +// monsalvo2012cn +// Subjects=23 +30 -45 -9 +30 -63 -6 +33 -81 9 +-27 -48 -9 +-27 -90 9 +-24 -84 -9 +39 -51 -15 +42 -81 -9 +-39 -60 -15 +-39 -84 -3 + +// okamoto2017ad +// Subjects=12 +-50 -68 0 +54 -74 0 +-48 -24 36 +32 -48 58 +42 52 -18 +4 -56 28 +42 20 -32 +-22 -8 -14 +18 -6 -12 +40 -72 38 + +// passarotti2003td +// Subjects=12 +38 -40 -17 +-40 -40 -17 +58 -40 -9 +-58 40 -9 +50 -53 -17 +-52 -56 -17 +-58 -7 5 +-40 -20 -4 +-1 -25 24 +29 -35 42 +-24 -33 51 +-4 39 53 +-39 3 55 +5 19 -19 +60 21 20 diff --git a/nimare/resources/Enge2021_objects_talairach.txt b/nimare/resources/Enge2021_objects_talairach.txt new file mode 100644 index 000000000..01a77b37a --- /dev/null +++ b/nimare/resources/Enge2021_objects_talairach.txt @@ -0,0 +1,179 @@ +// Reference=Talairach +// aylward2005ba +// Subjects=11 +43 -44 -10 +-40 -66 -9 +39 -59 -8 +36 -68 9 +-49 -20 3 +7 13 46 + +// corbett2008af +// Subjects=15 +36 -56 19 +19 -8 -5 +-30 -78 -20 +23 -86 -20 + +// kersey2016do +// Subjects=29 +20 -70 -33 +-20 49 26 +-6 60 17 +-21 -21 58 +17 55 30 +6 61 16 +60 2 7 +53 31 5 +2 58 33 +-46 -8 -22 +-52 -11 -27 +-28 -28 -18 +-31 -15 -19 +31 -14 -25 +-20 -88 23 +16 -85 13 +-47 -69 -4 +32 -49 -6 +-43 -41 60 +23 -48 55 +-55 -23 28 +34 -4 1 +-43 -20 12 +-39 6 -27 +-40 -22 9 +-46 -2 -13 +-46 10 -24 +61 -11 12 +59 11 -4 +65 -14 -3 + +// libertus2008dc +// Subjects=15 +41 -53 -21 +15 -101 -7 +23 -98 -14 +-26 -86 -14 +-19 -90 -14 +-19 -98 -7 +4 41 -7 +4 19 -7 +-4 45 0 +-45 -53 -28 +-41 -49 -21 +8 -56 21 + + +// scherf2007vc: Adolscents +// Subjects=10 +39 -47 -22 +45 -74 1 +60 -49 9 +55 -4 -16 +10 -59 28 +-39 -70 18 +-47 17 -8 +39 25 -9 +5 54 44 +-6 -4 57 +-5 46 -12 +42 -9 50 +21 -2 54 +26 -66 46 +-11 -67 50 +28 -79 8 +-27 -85 19 +45 -55 -8 +-45 -60 -5 +18 -87 -6 +-13 -89 -5 +26 -40 -4 +-25 -48 -1 +-22 -73 53 +32 -52 51 +-14 -95 12 +-54 -34 33 +40 -60 -7 +-41 -57 -3 +11 -81 -3 +22 -73 -18 +-27 -73 -14 +33 -88 2 +-34 -5 32 + +// scherf2007vc: Children +// Subjects=10 +42 -68 -19 +-15 56 5 +14 -80 38 +-14 -76 51 +6 -41 25 +29 -75 31 +-22 -79 13 +21 -85 -5 +-22 -85 -3 +13 -86 -6 +-19 -94 -5 +19 -30 -18 +-28 -53 -6 +29 -53 49 +-21 -59 43 +-23 -82 37 +31 -70 20 +18 -94 -5 +-23 -86 28 +-9 -97 -15 +41 -72 -12 +-40 -60 -17 +22 -39 -14 +-21 -79 -24 + +// scherf2010ll (46) +// Subjects=10 +40 -41 -23 +-39 -51 -19 +50 -61 9 +55 -50 12 +49 -58 12 +-63 -30 -7 +-41 21 -31 +-39 -60 38 +-1 57 28 +-6 42 -4 +8 43 53 +21 20 49 +5 53 46 +0 35 53 +31 58 9 +-16 28 55 +-18 35 43 +-2 63 8 +33 3 34 +-45 6 51 +-48 28 -5 +-34 -73 -41 +26 -42 -8 +-24 -45 -8 +16 -84 -7 +-5 -87 -3 +30 -76 21 +-22 -82 18 +20 -67 58 +-9 -68 56 +62 -15 25 +58 6 25 +-31 13 12 +-39 31 15 +41 -61 -11 +-41 -66 -7 +23 -62 -12 +-24 -63 -12 +7 -81 0 +31 -80 7 +-22 -85 7 +34 -48 55 +-30 -54 53 +-55 -30 37 +59 -18 27 +-45 -31 21 +-44 30 17 diff --git a/nimare/resources/semantic_relatedness_children.txt b/nimare/resources/Enge2021_relatedness.txt similarity index 100% rename from nimare/resources/semantic_relatedness_children.txt rename to nimare/resources/Enge2021_relatedness.txt