Merge pull request #88 from FCP-INDI/dev0392

Doc update 8/16/16

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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+natomical_csf_mask, The CSF mask(s) produced by segmentation.  NifTIs are contained within a subdirectory of the form _csf_threshold_<threshold>.
+anatomical_gm_mask, The gray matter mask(s) produced by segmentation.  NifTIs are contained within a subdirectory of the form _gm_threshold_<threshold>.
+anatomical_wm_mask, The white matter mask(s) produced by segmentation.  NifTIs are contained within a subdirectory of the form _gm_threshold_<threshold>.
+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/derivatives.csv

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+All Outputs
+alff
+falff
+centrality_outputs
+dr_tempreg_maps
+motion_correct
+reho
+sca_roi
+sca_seed
+sca_tempreg
+
+<derivative>_zstd, The z-score standardized output for a derivative (exception for VMHC- see VMHC table for more details).
+<derivative>_zstat, The z-score standardized output for a derivative (used for SCA and dual regression; means something different for VMHC - see VMHC table for more details).
+<derivative>_fisher_zstd - The z-score standardized output for a derivative using Fisher's z-score transformation.
+output_means, A directory containing a series of nested sub-directories of the following form (with subdirectories representing optional steps only included if those steps were run): _scan_rest/_csf_threshold_<threshold>/_gm_threshold_<threshold>/_wm_threshold_<threshold>/<nuisance_regressors>/_hp_<high frequency cut-off>/_lp_<low frequency cut off>/.  At the lowest level of these subdirectories are text files that contain the average values for each derivative run.  These individual means are also aggregated into a single file of the form 'output_means_<subject name>.csv' in the individua subject output directory.
+<output>_to_standard, A derivative or other intermediate output transformed into MNI space.
+
+Smoothing
+<derivative>_smooth,  directory containing a series of nested sub-directories of the following form (with subdirectories representing optional steps only included if those steps were run): _scan_rest/_csf_threshold_<threshold>/_gm_threshold_<threshold>/_wm_threshold_<threshold>/<nuisance_regressors>/_hp_<high frequency cut-off>/_lp_<low frequency cut off>/_fwhm_<kernel_fwhm>.  At the lowest level of these subdirectories are smoothed NifTI files.
+
+Seed-based Correlation Analysis (SCA) - Analyze the connectivity between brain regions.
+sca_roi_correlation_files, The results of seed-based correlation analysis for extracted time series from ROIs using 3dTcorr1D.  Results for multiple ROIs are contained in separate files.
+sca_roi_correlation_stack, The results of seed-based correlation analysis for extracted time series from ROIs using 3dTcorr1D.  Results for ROIs are concatenated together into a single 4D NifTI file.
+sca_seed_correlation_files, The results of seed-based correlation analysis for extracted time series from seed specifications using 3dTcorr1D.
+sca_tempreg_maps_files, The results of multiple regression seed-based correlation analysis for extracted time series from ROIs.  GLM parameter estimate images for each timeseries in the input file. Results for multiple ROIs are contained in separate files.
+sca_tempreg_maps_stack, The results of multiple regression seed-based correlation analysis for extracted time series from ROIs.  GLM parameter estimate images for each timeseries in the input file. Results for ROIs are concatenated together into a single 4D NifTI file.
+
+Dual Regression - Compare large-scale networks.
+spatial_map_timeseries, The GLM-derived time series associated with voxels in a spatial map for the participant.
+dr_tempreg_maps_files, The subject-specific spatial maps generated by running temporal regression.  Results for multiple regions in the spatial map are contained in separate files.
+dr_tempreg_maps_stack, The subject-specific spatial maps generated by running temporal regression.  Results for multiple regions in the spatial map are concatenated together into a single 4D NifTI file.
+
+Voxel-mirrored Homotopic Connectivity (VMHC) - Investigate connectivity between hemispheres.
+vmhc_fisher_zstd_zstat_map, The Z statistic map for VMHC.
+vmhc_fisher_zstd, The Fisher Z transfrom map for VMHC.
+vmhc_raw_score, The VMHC results in a 3D NifTI file.
+
+Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (fALFF) - Measure the power of slow fluctuations in brain activity.
+alff_img, The ALFF results in a 3D NifTI file.
+falff_img, The f/ALFF results in a 3D NifTI file.
+
+Regional Homogeneity (ReHo) - Measure the similarity of activity patterns across neighboring voxels.
+raw_reho_map, The results for ReHo in a 3D NifTI file.
+
+Network Centrality - Analyze the structure of functional networks.
+centrality_outputs, A directory containing degree centrality, eigenvector centrality, and lfcd results as NifTI files.

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

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+Functional Preprocessing
+raw_functional, A copy of the resting-state data for the current participant.
+slice_time_corrected, The slice time corrected functional image.
+coordinate_transformation
+functional_brain_mask
+functional_freq_filtered
+functional_mni, The functional image transformed into MNI space.
+functional_preprocessed_mask
+functional_to_anat_linear_xfm, The transformation matrix used by FSL to co-register the functional image to the subject's T1 image.
+mean_functional, The mean functional image.
+mean_functional_in_anat, The mean functional image co-registered to the individual subject's T1 image.
+mean_functional_in_mni, The mean functional image transformed into the MNI space.
+selected_func_volume
+itk_collected_warps_%s
+itk_func_anat_affine_%s
+preprocessed
+
+Nuisance Corrections
+motion_correct, The motion-corrected functional data.
+functional_median_angle_corrected, Functional data with the median angle correction applied.
+functional_nuisance_residuals, A file containing the residuals from nuisance regression.
+
+Temporal Filtering
+bandpassed_file, The functional data after applying band-pass filtering in the pipeline.
+
+Motion Correction
+frame_wise_displacement
+max_displacement
+power_params
+motion_params
+movement_parameters
+scrubbed_preprocessed
+scrubbing_frames_excluded
+scrubbing_frames_included
+scrubbing_movement_parameters
+
+Time Series Extraction
+voxel_timeseries, The extracted time series for a coordinate-defined seed.
+voxel_timeseries_for_SCA, The extracted time series for a coordinate-defined seed as used by seed-based correlation analysis.
+roi_timeseries, The extracted time series for an ROI as used by seed-based correlation analysis.
+roi_timeseries_for_SCA, The extracted time series for an ROI as used by seed-based correlation analysis.
+
+Quality Control
+qc___csf_gm_wm_a
+qc___csf_gm_wm_s
+qc___fd_plot
+qc___mean_func_with_mni_edge_a
+qc___mean_func_with_mni_edge_s
+qc___mean_func_with_t1_edge_a
+qc___mean_func_with_t1_edge_s
+qc___mni_normalized_anatomical_a
+qc___mni_normalized_anatomical_s
+qc___movement_rot_plot
+qc___movement_trans_plot
+qc___%s_a%measure
+qc___%s_hist%measure
+qc___skullstrip_vis_a
+qc___skullstrip_vis_s
+qc___snr_a
+qc___snr_hist
+qc___snr_s
+qc___snr_val
+qc___%s_s%measure

docs/user/_sources/cloud.txt

@@ -6,29 +6,23 @@ Introduction
 
 The C-PAC team has released an Amazon Marketplace AMI, making it easier for researchers to use C-PAC in the cloud.  You can use the AMI to either launch a single machine for basic runs or create a high performance computing (HPC) cluster using Starcluster.  Clusters can be dynamically scaled up as your computational needs increase.  Detailed explanations of cloud computing and HPC are beyond the scope of this documentation, but we will define a few key terms before we start.  If these terms are familiar, you may skip them and proceed to later sections.
 
-* Amazon Machine Instance (AMI) - A disk image of an operating system and any additional installed software that can be used to create a virtual machine. 
+* **Amazon Machine Instance (AMI)** - A disk image of an operating system and any additional installed software that can be used to create a virtual machine. 
 
-* Instance - A single running virtual machine whose initial state is based on the AMI that it is launched from.  Instances can be classified as spot instances or on-demand instances.  On-demand instances are reliably created the moment they are requested for a fixed rate.  Spot instances are created based on whether or not a bid that you set is accepted by Amazon.  They can be significantly cheaper than on-demand instances, but are only created when Amazon accepts your bid.
+* **Instance** - A single running virtual machine whose initial state is based on the AMI that it is launched from.  Instances can be classified as spot instances or on-demand instances.  On-demand instances are reliably created the moment they are requested for a fixed rate.  Spot instances are created based on whether or not a bid that you set is accepted by Amazon.  They can be significantly cheaper than on-demand instances, but are only created when Amazon accepts your bid.
 
-* Instance Type - The hardware specification for a given instance. A list of the instance types made available by Amazon may be found `here <http://aws.amazon.com/ec2/instance-types>`_.
+* **Instance Type** - The hardware specification for a given instance. A list of the instance types made available by Amazon may be found `here <http://aws.amazon.com/ec2/instance-types>`_.
 
-* Terminated Instance - An instance is considered terminated when its resources have been completely freed up for use by others in the Amazon cloud.  Any data on a terminated instance that is not relocated to persistent storage such as EBS (see below) will be completely discarded.  Instance termination is the virtual equivalent of throwing out a physical server.  When you have terminated an instance, you are no longer paying for it.  Note that by default, instances do not have persistent storage attached to them- you will need to configure persistent storage when you set up the instance.
+* **Terminated Instance** - An instance is considered terminated when its resources have been completely freed up for use by others in the Amazon cloud.  Any data on a terminated instance that is not relocated to persistent storage such as EBS (see below) will be completely discarded.  Instance termination is the virtual equivalent of throwing out a physical server.  When you have terminated an instance, you are no longer paying for it.  Note that by default, instances do not have persistent storage attached to them- you will need to configure persistent storage when you set up the instance.
 
-* Stopped Instance - An instance is considered stopped when it is not active, but its resources are still available for future use whenever you choose to reactivate it.  Stopping an instance is the virtual equivalent of turning a computer off or putting it in hibernate mode.  When you stop an instance, you continue to pay for the storage associated with it (i.e., the main and other volumes attached to it), but not for the instance itself.  You should stop an instance when the analyses you are working on are not fully done and you would like to preserve the current state of a running instance.
+* **Stopped Instance** - An instance is considered stopped when it is not active, but its resources are still available for future use whenever you choose to reactivate it.  Stopping an instance is the virtual equivalent of turning a computer off or putting it in hibernate mode.  When you stop an instance, you continue to pay for the storage associated with it (i.e., the main and other volumes attached to it), but not for the instance itself.  You should stop an instance when the analyses you are working on are not fully done and you would like to preserve the current state of a running instance.
 
-* Simple Storage Service (S3) - A form of storage offered by Amazon.  S3 is not intended to be directly attached to instances since it lacks a filesystem, but it can be used to archive large datasets.  Amazon provides tools for uploading data to S3 'buckets' where it can be stored.  It is less costly than EBS.
+* **Simple Storage Service (S3)** - A form of storage offered by Amazon.  S3 is not intended to be directly attached to instances since it lacks a filesystem, but it can be used to archive large datasets.  Amazon provides tools for uploading data to S3 'buckets' where it can be stored.  It is less costly than EBS.
 
-* Elastic Block Storage (EBS) - A form of persistent storage offered by Amazon for use with instances.  When you have terminated an instance, items stored in an EBS volume can be accessed by any future instances that you start up.
+* **Elastic Block Storage (EBS)** - A form of persistent storage offered by Amazon for use with instances.  When you have terminated an instance, items stored in an EBS volume can be accessed by any future instances that you start up.
 
-* EC2 Instance Store - A form of temporary storage that comes included with some instance types.  Instance store volumes must be added manually before launching an instance, and all files stored on them will be lost when the instance is terminated.  The instance store is typically mounted at ``/mnt``.
+* **EC2 Instance Store** - A form of temporary storage that comes included with some instance types.  Instance store volumes must be added manually before launching an instance, and all files stored on them will be lost when the instance is terminated.  The instance store is typically mounted at ``/mnt``.
 
-* Head Node - The primary node of an HPC cluster, to which all other nodes are connected.  The head node will run a job scheduler (such as Sun Grid Engine) to allocate jobs to the other nodes. 
-
-* Worker Node - A node in an HPC cluster to which tasks are delegated by the head node via a job scheduler.
-
-* Job Scheduler - A program that can allocate computational resources in an HPC cluster to jobs based on availability and distribute jobs across nodes. The C-PAC AMI uses Sun Grid Engine (SGE) as its job scheduler.
-
-* Job Submission Script - A shell script with a series of commands to be executed as part of the job.  Submission scripts may also include flags that activate functionality specific to the scheduler.
+Lastly, it would be import to review any terms related to :doc:`the Sun Grid Engine job scheduler <compute_config>`.
 
 Creating AWS Access and Network Keys
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -345,5 +339,4 @@ Additional Links
 ^^^^^^^^^^^^^^^^
 
 * `The StarCluster User Manual <http://star.mit.edu/cluster/docs/latest/manual/index.html>`_
-* `The Sun Grid Engine User Guide <http://www.csb.yale.edu/userguides/sysresource/batch/doc/UserGuide_6.1.pdf>`_
 * `Getting Started with AWS <http://docs.aws.amazon.com/gettingstarted/latest/awsgsg-intro/gsg-aws-intro.html>`_