Conversion to Launching CCF Pipelines with FreeSurfer v6

• Use credentials files instead of security files
• Pull shadow numbers out of scripts and have the range of shadow numbers specified by environment variables that are specified when setting up for the DB to use
• Make changes for using FreeSurfer v6

Final code used for actual 7T HCP Packaging

Includes options in packaging scripts to:

• Block overwriting of already existing packages.

  This allows easy submission of CreateAllPackages jobs for subjects that have some but not all of the packages already existing. The existing packages will not be overwritten, and the non-existing packages will be created.

• Ignore missing files in package creation.

  The standard operating procedure for the packaging scripts is to abort and report an error if a file that is expected to be placed in a package is not found. An option was added to the packaging scripts to change this behavior so that packages can be created for subjects for which MSMAll processing could not be done because they do not have appropriate prerequisite scans.

Change queue for packaging jobs

v1.13.1

Tagging v1.13.1

Released for packaging 7T HCP data

This release was created to use for packaging the 7T HCP data for its re-release.

DeDriftAndResample 7T Mulitrun ICA+FIX High Resolution

v1.12.0

Tagging v1.12.0

Repair 7T High Resolution ICAFIX processing

The previous ICA+FIX processing done for the 7T High Resolution (1.6mm) data was done incorrectly.

The invocation of the ReApplyFixPipeline.sh script which was done to perform this processing expected its input Atlas dense time series file to be named <scan_name>_Atlas_MSMSulc.59k.dtseries.nii. However the actual file produced by the 7T Functional Preprocessing was named <scan_name>_Atlas.59k.dtseries.nii. Instead of objecting to not finding a <scan_name>_Atlas_MSMSulc.59k.dtseries.nii file, both the ReApplyFixPipeline.sh script and the corresponding MATLAB code that it calls, simply forged ahead with processing, did not report an error, and did not produce the correct output.

To confuse matters even a bit more, in order to follow a naming convention that was decided upon after the 7T Functional Preprocessing was completed, the file named <scan_name>_Atlas_59k.dtseries.nii was renamed via a patch process to <scan_name>_Atlas_1.6mm.dtseries.nii.

To repair this problem, a separate 7T processing pipeline was created (RepairIcaFixProcessingHCP7T to:

1. Retrieve the results of 7T Functional Preprocessing
2. Rename the <scan_name>_Atlas_1.6mm.dtseries.nii file to <scan_name>_Atlas_MSMSulc.59k.dtseries.nii as is expected by the ReApplyFixPipeline.sh script.
3. Re-invoke the ReApplyFixPipeline.sh script to generate a file named <scan_name>_Atlas_MSMSulc.59k_hp2000_clean.dtseries.nii
4. Rename the <scan_name>_Atlas_MSMSulc.59k_hp2000_clean.dtseries.nii file to follow the naming convention. So that file is renamed to <scan_name>_Atlas_1.6mm_hp2000_clean.dtseries.nii

This release contains the changes to launching scripts for that repair processing.

DeDriftAndResample of 7T Multirun ICA+FIX data

This release is for DeDriftAndResample of 7T data including results of Multirun ICA+FIX.

PostFix Completion Checking after 7T Multi-run ICA+FIX

The PostFix completion checking code only worked properly when PostFix was run on ICA+FIX processed data that was not produced using the Multi-run ICA+FIX processing.

The changes in this release make PostFix completion checking work for both Multi-run ICA+FIX processed data and for non-multi-run ICA+FIX processed data.

7T CinaB-Style Data Retrieval Update

Got 7T CinaB-style data retrieval to work for Multirun ICA+FIX results and PostFix results.

Multirun ICA+FIX on 7T Retinotopy Data - Bugfix 1

Changed processors per node request amount for Multirun ICA+FIX on 7T Retinotopy Data