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b-heifets committed Jun 10, 2024
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<article class="bd-article">

<h1>All modules for which code is available</h1>
<ul><li><a href="unravel/cluster_stats/brain_model.html">unravel.cluster_stats.brain_model</a></li>
<li><a href="unravel/cluster_stats/crop_clusters.html">unravel.cluster_stats.crop_clusters</a></li>
<li><a href="unravel/cluster_stats/effect_sizes/effect_sizes.html">unravel.cluster_stats.effect_sizes.effect_sizes</a></li>
<li><a href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html">unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute</a></li>
<li><a href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html">unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative</a></li>
<li><a href="unravel/cluster_stats/fdr.html">unravel.cluster_stats.fdr</a></li>
<li><a href="unravel/cluster_stats/fdr_range.html">unravel.cluster_stats.fdr_range</a></li>
<li><a href="unravel/cluster_stats/find_incongruent_clusters.html">unravel.cluster_stats.find_incongruent_clusters</a></li>
<li><a href="unravel/cluster_stats/group_bilateral_data.html">unravel.cluster_stats.group_bilateral_data</a></li>
<li><a href="unravel/cluster_stats/index.html">unravel.cluster_stats.index</a></li>
<li><a href="unravel/cluster_stats/legend.html">unravel.cluster_stats.legend</a></li>
<li><a href="unravel/cluster_stats/org_data.html">unravel.cluster_stats.org_data</a></li>
<li><a href="unravel/cluster_stats/prism.html">unravel.cluster_stats.prism</a></li>
<li><a href="unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html">unravel.cluster_stats.recursively_mirror_rev_cluster_indices</a></li>
<li><a href="unravel/cluster_stats/stats.html">unravel.cluster_stats.stats</a></li>
<li><a href="unravel/cluster_stats/stats_table.html">unravel.cluster_stats.stats_table</a></li>
<li><a href="unravel/cluster_stats/sunburst.html">unravel.cluster_stats.sunburst</a></li>
<li><a href="unravel/cluster_stats/table.html">unravel.cluster_stats.table</a></li>
<li><a href="unravel/cluster_stats/valid_clusters_summary.html">unravel.cluster_stats.valid_clusters_summary</a></li>
<li><a href="unravel/cluster_stats/validate_clusters.html">unravel.cluster_stats.validate_clusters</a></li>
<li><a href="unravel/core/argparse_utils.html">unravel.core.argparse_utils</a></li>
<li><a href="unravel/core/argparse_utils_rich.html">unravel.core.argparse_utils_rich</a></li>
<ul><li><a href="unravel/core/argparse_utils.html">unravel.core.argparse_utils</a></li>
<li><a href="unravel/core/config.html">unravel.core.config</a></li>
<li><a href="unravel/core/img_io.html">unravel.core.img_io</a></li>
<li><a href="unravel/core/img_tools.html">unravel.core.img_tools</a></li>
<li><a href="unravel/core/utils.html">unravel.core.utils</a></li>
<li><a href="unravel/image_io/h5_to_tifs.html">unravel.image_io.h5_to_tifs</a></li>
<li><a href="unravel/image_io/img_io.html">unravel.image_io.img_io</a></li>
<li><a href="unravel/image_io/img_to_npy.html">unravel.image_io.img_to_npy</a></li>
<li><a href="unravel/image_io/nii_hd.html">unravel.image_io.nii_hd</a></li>
<li><a href="unravel/image_io/nii_info.html">unravel.image_io.nii_info</a></li>
<li><a href="unravel/image_io/nii_io.html">unravel.image_io.nii_io</a></li>
<li><a href="unravel/image_io/nii_to_tifs.html">unravel.image_io.nii_to_tifs</a></li>
<li><a href="unravel/image_io/nii_to_zarr.html">unravel.image_io.nii_to_zarr</a></li>
<li><a href="unravel/image_io/reorient_nii.html">unravel.image_io.reorient_nii</a></li>
<li><a href="unravel/image_io/tif_to_tifs.html">unravel.image_io.tif_to_tifs</a></li>
<li><a href="unravel/image_io/zarr_to_nii.html">unravel.image_io.zarr_to_nii</a></li>
<li><a href="unravel/image_tools/atlas/relabel_nii.html">unravel.image_tools.atlas.relabel_nii</a></li>
<li><a href="unravel/image_tools/atlas/wireframe.html">unravel.image_tools.atlas.wireframe</a></li>
<li><a href="unravel/image_tools/avg.html">unravel.image_tools.avg</a></li>
<li><a href="unravel/image_tools/bbox.html">unravel.image_tools.bbox</a></li>
<li><a href="unravel/image_tools/extend_image.html">unravel.image_tools.extend_image</a></li>
<li><a href="unravel/image_tools/max.html">unravel.image_tools.max</a></li>
<li><a href="unravel/image_tools/pad_img.html">unravel.image_tools.pad_img</a></li>
<li><a href="unravel/image_tools/spatial_averaging.html">unravel.image_tools.spatial_averaging</a></li>
<li><a href="unravel/image_tools/tif_DoG.html">unravel.image_tools.tif_DoG</a></li>
<li><a href="unravel/image_tools/tif_rb.html">unravel.image_tools.tif_rb</a></li>
<li><a href="unravel/image_tools/transpose_axes.html">unravel.image_tools.transpose_axes</a></li>
<li><a href="unravel/image_tools/uniq_intensities.html">unravel.image_tools.uniq_intensities</a></li>
<li><a href="unravel/region_stats/regional_IF_mean_intensities.html">unravel.region_stats.regional_IF_mean_intensities</a></li>
<li><a href="unravel/region_stats/regional_IF_mean_intensities_in_segmented_voxels.html">unravel.region_stats.regional_IF_mean_intensities_in_segmented_voxels</a></li>
<li><a href="unravel/region_stats/regional_IF_mean_intensities_summary.html">unravel.region_stats.regional_IF_mean_intensities_summary</a></li>
<li><a href="unravel/region_stats/regional_cell_densities.html">unravel.region_stats.regional_cell_densities</a></li>
<li><a href="unravel/region_stats/regional_cell_densities_summary.html">unravel.region_stats.regional_cell_densities_summary</a></li>
<li><a href="unravel/region_stats/regional_counts.html">unravel.region_stats.regional_counts</a></li>
<li><a href="unravel/region_stats/regional_volumes.html">unravel.region_stats.regional_volumes</a></li>
<li><a href="unravel/register/ANTsPy_affine_initializer.html">unravel.register.ANTsPy_affine_initializer</a></li>
<li><a href="unravel/register/check_brain_mask.html">unravel.register.check_brain_mask</a></li>
<li><a href="unravel/register/check_reg.html">unravel.register.check_reg</a></li>
<li><a href="unravel/register/metadata.html">unravel.register.metadata</a></li>
<li><a href="unravel/register/prep_reg.html">unravel.register.prep_reg</a></li>
<li><a href="unravel/register/reg.html">unravel.register.reg</a></li>
<li><a href="unravel/segment/brain_mask.html">unravel.segment.brain_mask</a></li>
<li><a href="unravel/segment/copy_tifs.html">unravel.segment.copy_tifs</a></li>
<li><a href="unravel/segment/ilastik_pixel_classification.html">unravel.segment.ilastik_pixel_classification</a></li>
<li><a href="unravel/utilities/aggregate_files_from_sample_dirs.html">unravel.utilities.aggregate_files_from_sample_dirs</a></li>
<li><a href="unravel/utilities/aggregate_files_w_recursive_search.html">unravel.utilities.aggregate_files_w_recursive_search</a></li>
<li><a href="unravel/utilities/clean_tif_dirs.html">unravel.utilities.clean_tif_dirs</a></li>
<li><a href="unravel/utilities/prepend_conditions.html">unravel.utilities.prepend_conditions</a></li>
<li><a href="unravel/utilities/rename.html">unravel.utilities.rename</a></li>
<li><a href="unravel/utilities/toggle_samples.html">unravel.utilities.toggle_samples</a></li>
<li><a href="unravel/voxel_stats/apply_mask.html">unravel.voxel_stats.apply_mask</a></li>
<li><a href="unravel/voxel_stats/hemi_to_LR_avg.html">unravel.voxel_stats.hemi_to_LR_avg</a></li>
<li><a href="unravel/voxel_stats/mirror.html">unravel.voxel_stats.mirror</a></li>
<li><a href="unravel/voxel_stats/prep_vstats.html">unravel.voxel_stats.prep_vstats</a></li>
<li><a href="unravel/voxel_stats/vstats.html">unravel.voxel_stats.vstats</a></li>
<li><a href="unravel/voxel_stats/whole_to_LR_avg.html">unravel.voxel_stats.whole_to_LR_avg</a></li>
<li><a href="unravel/voxel_stats/z_score.html">unravel.voxel_stats.z_score</a></li>
<li><a href="unravel/warp/to_atlas.html">unravel.warp.to_atlas</a></li>
<li><a href="unravel/warp/to_native.html">unravel.warp.to_native</a></li>
<li><a href="unravel/warp/warp.html">unravel.warp.warp</a></li>
</ul>

</article>
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<h1 id="index">Index</h1>

<div class="genindex-jumpbox">
<a href="#A"><strong>A</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>

</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.core.html#unravel.core.config.AttrDict">AttrDict (class in unravel.core.config)</a>
</li>
</ul></td>
</tr></table>

<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.core.html#unravel.core.config.Config">Config (class in unravel.core.config)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.core.html#unravel.core.config.Configuration">Configuration (class in unravel.core.config)</a>
</li>
</ul></td>
</tr></table>

<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.utilities.html#unravel.utilities.aggregate_files_w_recursive_search.find_and_copy_files">find_and_copy_files() (in module unravel.utilities.aggregate_files_w_recursive_search)</a>
</li>
</ul></td>
</tr></table>

<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.utilities.html#unravel.utilities.aggregate_files_w_recursive_search.main">main() (in module unravel.utilities.aggregate_files_w_recursive_search)</a>
</li>
<li>
module

<ul>
<li><a href="unravel.cluster_stats.html#module-unravel.cluster_stats">unravel.cluster_stats</a>
</li>
<li><a href="unravel.cluster_stats.effect_sizes.html#module-unravel.cluster_stats.effect_sizes">unravel.cluster_stats.effect_sizes</a>
</li>
<li><a href="unravel.core.html#module-unravel.core">unravel.core</a>
</li>
<li><a href="unravel.core.html#module-unravel.core.argparse_utils">unravel.core.argparse_utils</a>
</li>
<li><a href="unravel.core.html#module-unravel.core.config">unravel.core.config</a>
</li>
<li><a href="unravel.image_io.html#module-unravel.image_io">unravel.image_io</a>
</li>
<li><a href="unravel.image_tools.html#module-unravel.image_tools">unravel.image_tools</a>
</li>
<li><a href="unravel.image_tools.atlas.html#module-unravel.image_tools.atlas">unravel.image_tools.atlas</a>
</li>
<li><a href="unravel.region_stats.html#module-unravel.region_stats">unravel.region_stats</a>
</li>
<li><a href="unravel.register.html#module-unravel.register">unravel.register</a>
</li>
<li><a href="unravel.segment.html#module-unravel.segment">unravel.segment</a>
</li>
<li><a href="unravel.utilities.html#module-unravel.utilities">unravel.utilities</a>
</li>
<li><a href="unravel.utilities.html#module-unravel.utilities.aggregate_files_w_recursive_search">unravel.utilities.aggregate_files_w_recursive_search</a>
</li>
<li><a href="unravel.voxel_stats.html#module-unravel.voxel_stats">unravel.voxel_stats</a>
</li>
<li><a href="unravel.warp.html#module-unravel.warp">unravel.warp</a>
</li>
</ul></li>
</ul></td>
</tr></table>

<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.utilities.html#unravel.utilities.aggregate_files_w_recursive_search.parse_args">parse_args() (in module unravel.utilities.aggregate_files_w_recursive_search)</a>
</li>
</ul></td>
</tr></table>

<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.core.html#unravel.core.argparse_utils.SM">SM (class in unravel.core.argparse_utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.core.html#unravel.core.argparse_utils.SuppressMetavar">SuppressMetavar (class in unravel.core.argparse_utils)</a>
</li>
</ul></td>
</tr></table>

<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
unravel.cluster_stats

<ul>
<li><a href="unravel.cluster_stats.html#module-unravel.cluster_stats">module</a>
</li>
</ul></li>
<li>
unravel.cluster_stats.effect_sizes

<ul>
<li><a href="unravel.cluster_stats.effect_sizes.html#module-unravel.cluster_stats.effect_sizes">module</a>
</li>
</ul></li>
<li>
unravel.core

<ul>
<li><a href="unravel.core.html#module-unravel.core">module</a>
</li>
</ul></li>
<li>
unravel.core.argparse_utils

<ul>
<li><a href="unravel.core.html#module-unravel.core.argparse_utils">module</a>
</li>
</ul></li>
<li>
unravel.core.config

<ul>
<li><a href="unravel.core.html#module-unravel.core.config">module</a>
</li>
</ul></li>
<li>
unravel.image_io

<ul>
<li><a href="unravel.image_io.html#module-unravel.image_io">module</a>
</li>
</ul></li>
<li>
unravel.image_tools

<ul>
<li><a href="unravel.image_tools.html#module-unravel.image_tools">module</a>
</li>
</ul></li>
<li>
unravel.image_tools.atlas

<ul>
<li><a href="unravel.image_tools.atlas.html#module-unravel.image_tools.atlas">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
unravel.region_stats

<ul>
<li><a href="unravel.region_stats.html#module-unravel.region_stats">module</a>
</li>
</ul></li>
<li>
unravel.register

<ul>
<li><a href="unravel.register.html#module-unravel.register">module</a>
</li>
</ul></li>
<li>
unravel.segment

<ul>
<li><a href="unravel.segment.html#module-unravel.segment">module</a>
</li>
</ul></li>
<li>
unravel.utilities

<ul>
<li><a href="unravel.utilities.html#module-unravel.utilities">module</a>
</li>
</ul></li>
<li>
unravel.utilities.aggregate_files_w_recursive_search

<ul>
<li><a href="unravel.utilities.html#module-unravel.utilities.aggregate_files_w_recursive_search">module</a>
</li>
</ul></li>
<li>
unravel.voxel_stats

<ul>
<li><a href="unravel.voxel_stats.html#module-unravel.voxel_stats">module</a>
</li>
</ul></li>
<li>
unravel.warp

<ul>
<li><a href="unravel.warp.html#module-unravel.warp">module</a>
</li>
</ul></li>
</ul></td>
</tr></table>

<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="unravel.core.html#unravel.core.config.Configuration.verbose">verbose (unravel.core.config.Configuration attribute)</a>
</li>
</ul></td>
</tr></table>



</article>
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