fcp-indi / fcp-indi.github.io Goto Github PK

Some users would like to use C-PAC without the GUI, so we should have a tutorial explaining how to put together a subject list, pipeline configuration without the GUI.

Specifically, how to upload data to Amazon.

See:
FCP-INDI/C-PAC#445

Environmental variables should be defined in .bashrc and then .bashrc should be sourced by .bash_profile. Apparently all new terminal windows in OS X have login shells. Thanks Obama.

It doesn't seem like pipelines are actually named after places (though pipeline_names.py exists in utils). If pipeline_names.py isn't actually used any more, this section should be updated to reflect that.

The current screenshot for the subject list setup does not have the 'Subject List Name' field. Also, it may be good to add a screenshot for 'Defining File Path Templates'.

For the next documentation update, make sure that these files will still work as downloaded with the subject builder.

http://docutils.sourceforge.net/docs/ref/rst/directives.html#csv-table

Describe how sometimes Cython can cause execution of pipelines to stall in versions of C-PAC using Cython.

Located at:
docs/user/compute_config.html

Namely:
Outputs and Measures -> Seed-based Correlation Analysis (SCA)
Outputs and Measures -> Connectome-wide Association Studies (CWAS)

Data Output -> Software Concepts -> Workflows:
"A complete list of workflows"

Under Motion Correction --> Regression of Motion Parameters

Users need to know this beforehand.

Make sure that users can configure a security group that only lets in certain IP addresses

Presently, it is unclear where QC pages are found in individual output directories and which window toggles on QC report generation.

See:

https://groups.google.com/forum/#!topic/cpax_forum/iybagHJvu98

For the GUI tutorials for individual modules, it might be best to show all possible options that can be toggled via pulldown menus. Steve has already done this for some sites, but others need to have this added. Namely:

"Outputs and Measures" -> "Data Preprocessing" -> "Anatomical Preprocessing"
"Outputs and Measures" -> "Data Preprocessing" -> "Motion Correction"
"Outputs and Measures" -> "Data Preprocessing" -> "Slice Timing Correction" (Actually, this doesn't even provide descriptions of the options. This will need to be added.)
"Outputs and Measures" -> "Data Preprocessing" -> "Nuisance Signal Regression" (Actually, this doesn't even provide descriptions of the options. This will need to be added.)
"Outputs and Measures" -> "Data Preprocessing" -> "Temporal Filtering"
"Outputs and Measures" -> "Data Preprocessing" -> "Spatial Smoothing"
"Outputs and Measures" -> "Connectivity Measures" -> "Dual Regression"
"Outputs and Measures" -> "Connectivity Measures" -> "Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (f/ALFF)"
"Outputs and Measures" -> "Connectivity Measures" -> "Voxel-Mirrored Homotopic Connectivity (VMHC)"
"Outputs and Measures" -> "Connectivity Measures" -> "Bootstrap Analysis of Stable Clusters (BASC)"
"Outputs and Measures" -> "Connectivity Measures" -> "Regional Homogeneity"
"Outputs and Measures" -> "Connectivity Measures" -> "Network Centrality"

m3.xlarge is minimum; c3.8xlarge or a c3.4xlarge is more typical for what you want

This can be a bit confusing for those unfamiliar with the codebase. See:
FCP-INDI/C-PAC#448

Briefly explain how nipype will not re-execute nodes if they have been run before (to avoid re-creating already existent output and wasting computational resources). Explain how this has sometimes been problematic when running data again between two different versions of C-PAC.

Just add the script that you found on the wxPython wiki- see framework build Python issue.

Currently, there's no good summary explaining how cpac_pipeline.py works with respect to the resource pool and strategy class. This would be something that would be good to add to the developer documentation.

C-PAC 0.3.9 will include a new field in its pipeline config YAML- 'ref_mask' -which is a user-specified reference mask for FNIRT. This feature was added because sometimes FNIRT .cnf files would erroneously not be overwritten, causing issues where incompatible resolutions were used in the pipeline.

use.html -> "Running Group-Level Analysis" -> "<ga_strategies.png>"
basc.html -> "Configuring CPAC to run Anatomical Registration" -> "images/basc_gui.png"

Which branch to pull from, where to merge changes, etc

http://www.frontiersin.org/10.3389/conf.fninf.2013.09.00042/event_abstract

Zuo et al (2010), which is cited in the user docs, weighs connectivity values based on grey matter probability but C-PAC does not. This a point that could be clarified in user/developer documentation.

The documentation needs a new screenshot of the network centrality pane.

The index has a Javascript applet that will load in Pickle/other files from a local temp directory that is most likely not on Github.

Jenkinson's

In the seg_preproc section at least, the hyperlinks for FSL command man files are broken.

If so we should add these to the page in the user docs.

-Include issues with 1 mm atlases and memory.
-wx issues on Mac (#43)

In data_config.html:

-'subject_list_gui.png' image embed is broken.
-At the end of 'Example File Path Templates'- what exactly do we provide?
-In general, it is very geared towards YAML configuration right now, with the GUI not really well-documented.

The hyperlink to Zang et al 2007 in the first paragraph includes an extra ' " ' appended to the end that breaks the link.

The help page (fcp-indi.github.io/docs/user/help.html) redirects users to the Github issue tracker when it should redirect them to the Google forum instead.

Currently:

inputspec.threshold_option: string (int)
threshold options: 0 for probability p_value, 1 for sparsity threshold, any other for threshold value

and

threshold_option : an integer
0 for probability p_value, 1 for sparsity threshold, 2 for actual threshold value, and 3 for no threshold and > fast approach

Looks like 2 for R threshold should be in one or both of these.

https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/network_centrality/resting_state_centrality.py#L831

See FCP-INDI/C-PAC#532

http://fcp-indi.github.io/docs/developer/workflows/group_analysis.html

Link for flameo is broken.

From Danny:

For the next release, 0.4.0, we've removed the AWS and cluster-submitting code from C-PAC and set it up > as its own project: https://github.com/FCP-INDI/INDI-Tools

It's pip install-able as well: https://pypi.python.org/pypi/INDI-Tools/0.0.5