Descriptions of anatomical outputs

Author: jpellman

docs/user/_sources/_static/outputs/anatomical/registration.csv

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+anatomical_reorient,The anatomical image re-oriented into RPI.
+anatomical_brain,The anatomical image re-oriented into RPI and skull-stripped (original intensities).
+anatomical_to_mni_linear_xfm, Affine matrix of the linear transformation from the individual's anatomical space to MNI space.
+mni_to_anatomical_linear_xfm, Affine matrix of the linear transformation from MNI space to the individual's anatomical space.
+anatomical_to_mni_nonlinear_xfm, The nonlinear field coefficients file of nonlinear transformation from the individual's anatomical space to MNI space.
+mni_to_anatomical_nonlinear_xfm, The nonlinear field coefficients file of nonlinear transformation from MNI space to the individual's anatomical space.
+mni_normalized_anatomical, The end result of applying the transformations to warp the RPI, skull-stripped brain in the individual's anatomical space to MNI space.
+anatomical_to_symmetric_mni_linear_xfm, Affine matrix of the linear transformation from the individual's anatomical space to a symmetric brain in MNI space (used for VMHC).
+symmetric_mni_to_anatomical_linear_xfm, Affine matrix of the linear transformation from a symmetric brain in MNI space to the individual's anatomical space (used for VMHC).
+anatomical_to_symmetric_mni_nonlinear_xfm, The nonlinear field coefficients file of nonlinear transformation from the individual's anatomical space to a symmetric brain in MNI space (used for VMHC).
+symmetric_mni_to_anatomical_nonlinear_xfm, The nonlinear field coefficients file of nonlinear transformation from a symmetric brain in MNI space to the individual's anatomical space (used for VMHC).
+symmetric_mni_normalized_anatomical, The end result of applying the transformations to warp the RPI, skull-stripped brain in the individual's anatomical space to a symmetric brain in MNI space (used for VMHC).
+ants_initial_xfm, The initial transformation matrix applied by ANTS to transform the individual's anatomical image to MNI space.
+ants_rigid_xfm, The rigid transformation matrix applied by ANTS to transform the individual's anatomical image to MNI space.
+ants_affine_xfm, The affine transformation matrix applied by ANTS to transform the individual's anatomical image to MNI space.
+anat_to_mni_ants_composite_xfm, The ANTS transformations concatenated together for transformation into MNI space.
+ants_symmetric_initial_xfm, The initial transformation applied by ANTS to transform the individual's anatomical image to an image in symmetric MNI space.
+ants_symmetric_rigid_xfm, The rigid transformation matrix applied by ANTS to transform the individual's anatomical image to an image in symmetric MNI space (used for VMHC).
+ants_symmetric_affine_xfm, The affine transformation matrix applied by ANTS to transform the individual's anatomical image to an image in symmetric MNI space (used for VMHC).
+anat_to_symmetric_mni_ants_composite_xfm, The ANTS transformations concatenated together for transformation into an image in symmetric MNI space (used for VMHC).
+
+

docs/user/_sources/_static/outputs/anatomical/segmentation.csv

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+anatomical_csf_mask, The CSF mask produced by segmentation.
+anatomical_gm_mask, The gray matter mask produced by segmentation.
+anatomical_wm_mask, The white matter mask produced by segmentation.
+seg_mixeltype, A mixeltype volume file (an output from brain segmentation using FAST).
+seg_partial_volume_files, Partial volume estimate files (outputs from brain segmentation using FAST).
+seg_partial_volume_map, The partial volume file (an output from brain segmentation using FAST).
+seg_probability_maps, Individual probability maps (output from brain segmentation using FAST).

docs/user/_sources/_static/outputs.csv renamed to docs/user/_sources/_static/outputs/outputs.csv

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-Anatomical Preprocessing
-anatomical_brain
-anatomical_csf_mask
-anatomical_gm_mask
-anatomical_reorient
-anatomical_to_mni_linear_xfm
-anatomical_to_mni_nonlinear_xfm
-anatomical_to_symmetric_mni_linear_xfm
-anatomical_to_symmetric_mni_nonlinear_xfm
-anatomical_wm_mask
-anat_to_mni_ants_composite_xfm
-anat_to_symmetric_mni_ants_composite_xfm
-ants_affine_xfm
-ants_initial_xfm
-ants_rigid_xfm
-ants_symmetric_affine_xfm
-ants_symmetric_initial_xfm
-ants_symmetric_rigid_xfm
-apply_ants_warp_func_mni
-apply_ants_warpoutputspec.output_image
-apply_fsl_warpout_file
-seg_mixeltype
-seg_partial_volume_files
-seg_partial_volume_map
-seg_probability_maps
-mni_normalized_anatomical
-mni_to_anatomical_linear_xfm
-mni_to_anatomical_nonlinear_xfm
-symmetric_mni_normalized_anatomical
-symmetric_mni_to_anatomical_linear_xfm
-symmetric_mni_to_anatomical_nonlinear_xfm
-
 Functional Preprocessing
 coordinate_transformation
 functional_brain_mask
@@ -147,6 +115,7 @@ qc___snr_val
 qc___%s_s%measure
 
 Derivatives Settings:
+#TODO Find out the names given to derivatives in cpac_pipline.py
 %s_fisher_zstd % output_resource
 %s_zstd % output_resource