dockerfile changes

• update docker file: new R version 3.6.3, python 3.7.4
• add new atlas #455 #456 #451 @mwvoss
• remove first x dummy volumes, optional #452 @mwvoss
• runing xcpengine on Slurm ##documentation @njheimbach

atlas in MNI2009

#381 #382

MNI2009a

Merge pull request #360 from a3sha2/master

MNI to MNI2009

compatible with fmriprep outputs of version 20.07

Merge pull request #336 from ariekahn/allow_res_tags

Allow for fmriprep resolution tags

update with fmriprpep 20.XX outputs

copy freesurfer from fmirprep/freesufer outputs or option to run fresh freesurfer if wanted::
. struc_process[cxt]=FSF-ACT - FSF for freesurfer
. include struc_freesurferdir[cxt]='path to freesufer dir in design file
. cifti files for cortical thickness and gmd are generated if FSF is included in the process.
. euler number in structural qc
qcanat activated and working!!!
QC for anatomical:

• euler_number_rh,euler_number_lh - Eurler number if freesurfer is included
• meanGMD - mean of Grey matter density
• SignalToNoiseRatio - grey matter signal to noise ratio
• BackgroundKurtosis - background intensity Kurtosis
• GreyMatterKurtosis - grey matter intensity Kurtosis
• EntropyFocusCriterion - entropy focus criterion ( for ghost signals)
• CorticalContrasts - coritical contrasts between white matter and grey matter signals
• FGBGEnergyRatio - Foreground-to-background energy ratio
• ContrastToNoiseRatio - contrast to noise ratio
• WhiteMatterSkewness - WhiteMatter Skewness
• BackgroundSkewness - background intensity Kurtosis
  JLF is configured for multi-parallelism option. this is useful for HPC and flywheel. the number of cpu cores can be specified in the design file: jlf_ncpu[cxt]=2 . 2 is default. Parallel configuration is much faster
  the documentation for jlf is activated, struc, gmd, task, qcanat and qc documentations are updated
  fcon design files are updated to remove framewise threshold where it is not needed. Only required for scrubbing.
  task confound can include other confound regressors other than basic 6 motion parameters ( check documentation ). Computing functional connectivity, reho and alff from task is also possible.
  if fmriprep output has freesurfer, ,the residualized bold and res4d (from task) are converted to cifti files as additional outputs.
  task,fcon documentation is updated
  acompcor selection from fmriprep version 20.XX - 5 CSF and 5 WM

freesurfer/struc/qcanat

copy freesurfer from fmirprep/freesufer outputs or option to run fresh freesurfer if wanted::
. struc_process[cxt]=FSF-ACT - FSF for freesurfer
. include struc_freesurferdir[cxt]='path to freesufer dir in design file
. cifti files for cortical thickness and gmd are generated if FSF is included in the process.
. euler number in structural qc
qcanat activated and working!!!
QC for anatomical:

• euler_number_rh,euler_number_lh - Eurler number if freesurfer is included
• meanGMD - mean of Grey matter density
• SignalToNoiseRatio - grey matter signal to noise ratio
• BackgroundKurtosis - background intensity Kurtosis
• GreyMatterKurtosis - grey matter intensity Kurtosis
• EntropyFocusCriterion - entropy focus criterion ( for ghost signals)
• CorticalContrasts - coritical contrasts between white matter and grey matter signals
• FGBGEnergyRatio - Foreground-to-background energy ratio
• ContrastToNoiseRatio - contrast to noise ratio
• WhiteMatterSkewness - WhiteMatter Skewness
• BackgroundSkewness - background intensity Kurtosis
  JLF is configured for multi-parallelism option. this is useful for HPC and flywheel. the number of cpu cores can be specified in the design file: jlf_ncpu[cxt]=2 . 2 is default. Parallel configuration is much faster
  the documentation for jlf is activated, struc, gmd, task, qcanat and qc documentations are updated
  fcon design files are updated to remove framewise threshold where it is not needed. Only required for scrubbing.
  task confound can include other confound regressors other than basic 6 motion parameters ( check documentation ). Computing functional connectivity, reho and alff from task is also possible.
  if fmriprep output has freesurfer, ,the residualized bold and res4d (from task) are converted to cifti files as additional outputs.
  task,fcon documentation is updated
  acompcor selection from fmriprep version 20.XX - 5 CSF and 5 WM

1.1.0

CBF computation with basil and scorescrub; distortion correction #204 #244 #102
Update the task modules for multisession and flywheel compatible #230 #245
Qc and flywheel documentation #241 #122
Added new atlases with correction for 7 and 17 community affiliations #247 #236 #222 #196 #202
restore the seed module #224 #213
different templates for frmiprep - MNI, PNC and OASIS - #235
new improved html report
update with fmriprep 1.5x and 20.x
cifti outputs for bold regressed data #323 #321

1.1.0rc2

Update prestats.mod

keeping up with new frmiprep version and documentations

Update the task modules for multisession #230 #245
added qc documentation #241 #122
complete asl modules added -cbf, basil and scorescrub #244 #204 #102
Added new atlases with correction for 7 and 17 community affiliations #247 #236 #222 #196 #202
restore the seed module #224 #213
different templates for frmiprep - MNI, PNC and OASIS - #235
separate spike regression (censor=1) and scrubbing (censor=2) #214 #246

version1.0

v1.0

[skip ci]