TaskfMRI Consolidation and Back out of FreeSurfer v6 requirement

This release includes:

1. Changes associated with #65 - Task fMRI analysis consolidation

   • Change Task fMRI Analysis pipeline to run with FSL version 5.0.7 or greater
   • No longer works with FSL version 5.0.6
   • Simplify file names since FSL version 5.0.6 is no longer supported
   • Remove files that are no longer needed since no longer supporting v5.0.6 and earlier

2. Back out changes introduced in v3.25.0 that were FreeSurfer v6 specific.

   • The version of FreeSurferPipeline.sh included in this release is the same as the one that was in v3.24.0.
   • It does not require FreeSurfer v6 and does not use the special version of the recon-all script.

3. Change to using "Pos" and "Neg" in file names for specification of phase encoding directions in Diffusion Preprocessing code instead of using RL and LR or PA and AP.

4. More consistently use EchoSpacing as a variable name instead of DwellTime in Functional Preprocessing code.

5. Changes associated with #66 - Don't include b0 files in merging of final data

6. Changes associated with #67 - Additions to consolidated TaskfMRILevel{1,2}.sh scripts

7. Some improved comments

NOTE

This release contains a version of PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonLinear.sh that uses an option on the Connectome Workbench command line tool (wb_command) that will be supported in Connectome Workbench v1.3.0. Using this release for Structural Preprocessing prior to the release of Connectome Workbench v1.3.0, will require the use of a development release of Connectome Workbench subsequent to v1.2.3.

DeDriftAndResample of 7T Multirun ICA+FIX High Resolution

This release is for DeDriftAndResample of 7T High Resolution (1.6mm) data including results of Multirun ICA+FIX.

It is not yet recommended that this release be used for Structural Preprocessing.

This release contains a version of FreeSurfer/FreeSurferPipeline.sh that requires a customized version of FreeSurfer v6, including a special version of the recon-all script that is not currently a released part of FreeSurver v6.

This release contains a version of PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh that uses an option on the Connectome Workbench command line tool (wb_command) that is not yet part of the released version of Connectome Workbench. The option being used is the -local-affine-method option of the -surface-distortion command. Support for this option will be included in Connectome Workbench version 1.3.0.

DeDriftAndResample of 7T Multirun ICA+FIX

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

It is not yet recommended that this release be used for Structural Preprocessing.

This release contains a version of PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh that uses an option on the Connectome Workbench command line tool (wb_command) that is not yet part of the released version of Connectome Workbench. The option being used is the -local-affine-method option of the -surface-distortion command. Support for this option will be included in Connectome Workbench version 1.3.0.

Multirun ICA+FIX on 7T Retinotopy Data

This release is intended to be used for running Multirun ICA+FIX processing on 7T Retinotopy data.

It is not yet recommended that this release be used for Structural Preprocessing.

This release contains a version of PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh that uses an option on the Connectome Workbench command line tool (wb_command) that is not yet part of the released version of Connectome Workbench. The option being used is the -local-affine-method option of the -surface-distortion command. Support for this option will be included in Connectome Workbench version 1.3.0.

New atlas files for fsaverage to fs_LR resampling

This release updates some files in the global/templates/standard_mesh_atlases/resample_fsaverage directory, and adds some new files. This improves the atlas to atlas registration for fsaverage contained in the resample_fsaverage directory.

Changes to MakeAverageDataset Pipeline for 2nd review

Supplemental/MakeAverageDataset/MakeAverageDataset.sh

Changes merged from pull request #36

1. Add -openmp flag to all calls to recon-all
2. Changes to work with volumes more efficiently
3. Readability improvements
4. Additional, optional arguments

Changes added after merge

1. Added support for positional specification of new arguments
2. Made sure main function does not use global variables set in the get_options function

Prepare ReApplyFix pipeline for v4.0.0 release

ReApplyFix/ReApplyFixPipeline.sh

1. Made sure it has a usage function that uses cat <<EOF
   a. Several of the parameter descriptions are still TBW
2. Have a get_options function that uses global variable names that are similar to the ones used in the main function yet are clearly recognizable as those set by the get_options function (names start with p_ for parameter)
3. main function gets its parameters positionally
4. main function uses local variables instead of global variables from the get_options function
5. All communication with the user (informational, debugging, or error messages) are via calls to log_* functions defined in a shared standard library of bash functions
6. Verification of the necessary environment variables is done "first thing" in the "global" (non-function) part of the script.
7. The global (non-function) part of the script checks for the use of positional or named parameters on the command line and only uses the get_options function if named parameters are used. This (along with some of the other changes above) allows invocation of the script using positional parameters or named parameters.
8. All references to the (unsupported) use of Octave instead of MATLAB have been removed.
9. Checks for environment variable MATLAB_COMPILER_RUNTIME if the MATLAB run mode is compiled MATLAB.
10. Defaults to using interpreted MATLAB

ReApplyFix/scripts/Compile_MATLAB_code.sh

1. This is a new file
2. It compiles the fix_3_clean.m MATLAB function for use by the ReApplyFixPipeline.sh script
3. It uses the MATLAB_HOME environment variable to determine what version of MATLAB to use for compiling.
4. It uses the ICAFIX environment variable to determine where file the fix_3_clean.m file to compile.

Notes about fix_3_clean.m

1. Previously, we had a copy of the fix_3_clean.m code from the ICAFIX release that was modified to not process volumetric data and was called fix_3_clean_no_vol.m. That file is no longer necessary because a parameter has been added to the fix_3_clean function in the latest version released with ICAFIX (v1.064) that controls whether volume processing is done or not. So the ReApplyFixPipeline.sh code has been updated to invoke the fix_3_clean MATLAB function differently depending upon whether we want volumetric processing to be done or not.
2. It also seems that the fix_3_clean.m version included with the latest release of ICAFIX (v1.064) includes the code to make the results the same regardless of whether a pre-v5.0.7 or post-v5.0.7 version of FSL is in use. That is, it takes care of the change in -bptf behavior introduced in FSL v5.0.7. It computes the mean, removes the mean before filtering, filters (-bptf), and then adds the mean back in.

Changes per review to DeDriftAndResamplePipeline.sh

Adopted a standard of specifying "NONE" for optional values when using positional parameters.

MakeAverageDataset pipeline prepared for v4.0.0 release

Main Script: Supplemental/MakeAverageDataset/MakeAverageDataset.sh

1. Made sure it has a usage function that uses cat <<EOF
   a. Although several of the parameter descriptions are still TBW
2. Have a get_options function that uses global variable names that are similar to the ones that are used in the main function yet are clearly recognizable as those set by the get_options function (names start with p_ for parameter)
3. main function gets its parameters positionally
4. main function uses local variables instead of global variables from the get_options function
5. All communication with the user (informational, debugging, or error messages) are via calls to log_* functions defined in a shared standard library of bash functions
6. Verification of the necessary environment variables is done "first thing" in the "global" (non-function) part of the script.
7. The global (non-function) part of the script checks for the use of positional or named parameters on the command line and only uses the get_options function if named parameters are used. This (along with some of the other changes above) allows invocation of the script using positional parameters or named parameters.

DeDriftAndResample pipeline prepared for v4.0.0 release

Prepared DeDriftAndResample Pipeline for v4.0.0 release

Main Script: DeDriftAndResample/DeDriftAndResamplePipeline.sh

1. Made sure it has a usage function that uses cat <<EOF
   a. Although several of the parameter descriptions are still TBW
2. Have a get_options function that uses global variable names that are similar to the ones that are used in the main function yet clearly recognizable as those set by the get_options function (names start with p_)
3. main function gets its parameters positionally
4. main function uses local variables instead of global variables from the get_options function
5. All communication with the user (informational and error messages) are via calls to log_* functions defined in a shared standard library of bash functions
6. Verification of the necessary environment variables is done "first thing" in the "global" (i.e. non-function) part of the script.
7. The global (non-function) part of the script checks for the user of positional or named parameters on the command line and only uses the get_options function if named parameters are used on the command line. This (along with some of the other changes above) allows invocation of the script using positional parameters on the command line if desired.
8. All references to the (unsupported) use of Octave instead of MATLAB have been removed
9. Checks for environment variable MATLAB_COMPILER_RUNTIME if the MATLAB run mode is compiled MATLAB
10. Defaults to using interpreted MATLAB

Tests run

"Run to completion" tests (not vetted results tests) have been performed using this release with a pipeline setup file configured to use the following tools:

• Customized version of FSL v5.0.9 - used by the ReApplyFixPipeline.sh script which is invoked by the DeDriftAndResamplePipeline.sh script.
  • "newer-than-released" version of bedpostx_gpu
  • "newer-than-released" version of eddy_cuda
  • "newer-than-released" version of melodic
• Connectome Workbench v1.2.3
• MATLAB R2016b - used by ReApplyFixPipeline.sh script which is invoked by the DeDriftAndResamplePipeline.sh script.