Fix to ciftify_meants and new ciftify_dlabel_to_vol script

[ENC] added new ciftify_dlabel_to_vol script to project surface-based labels into subject-specific nifti volume rois
[FIX] fixed bugs in ciftify_meants where the meants.csv was shorter than the labels if the labels were located in a location with no data. (Now will output a row of zero's for missing data).
[ENC] added many smoke tests related for ciftify_meants and ciftify_seed_corr functions
[FIX] updated the PINT test fixtures to correspond with newer nilearn image clean outputs (note: we now confirm that cifitfy_clean_img outputs should be different if for nilearn 0.5 and later (but slightly better)

Upgrading fmriprep base layer

[ENC] fmriprep base layer for fmriprep_cifitfy Docker is now 1.3.2
[ENC] nose dependancy removed from CI tests
[FIX] markdown to rest conversion of the long descriptor in the setup.py

2019-04-25 as described in NeuroImage

This is the final release before resubmitting revisions to NeuroImage. Enhancements include:

[ENC] adding the user an option in input a pre-calculated MNI transforms to ciftify_recon_all
[ENC] adding a new ciftify_falff script drafted by Delaney Johnson during her co-op term.

2019-04-04

Incremental bug fixes for ciftify_clean_img and cifti_vis_PINT.
[FIX] heatmaps in cifti_vis_PINT have white lines in correct place (in newer python)
[FIX] ciftify_clean_img doc string now clearer
[FIX] ciftify_clean_img does not assume that nifti TR's are in ms
[FIX] ciftify_clean_img now exits gracefully when confound.tsv input is missing
[FIX] all meants functions now don't exclude voxels/vertices with means of zero

Works with fmrirprep 1.3.0

[ENC] - bidsapp now has fmriprep:1.3.0.post2 as the base layer
[ENC] - bidsapp can now be set to read BIDS common derivatives from a specified path (with fmriprep turned off) using --read-from-derivatives option
[ENC] - bidsapp can also read old fmriprep (pre 1.2.0) derivatives with --older-fmriprep
[ENC] - bidsapp uses python 3.7 base with pybids 0.7.0

Now with FSL BBR

[ENC] - ciftify_subject_fmri now runs boundary-based registration if the --FLIRT-to-T1w flag is given (previously) this was FLIRT (corratio-based)

2.1.1 November 7 2018

[ENC] updating the fmriprep layer for the Docker to 1.1.8
[FIX] fixed MSM permissions within the docker
[DOC] finally mention BIDS-app and Docker in the documentation

cleaning up the workflow and fixed the t1w to 32k bug

• [FIX] cifti_vis_pint adjusted for ivertex-pvertex name change
• [FIX] ciftify_seedcorr and related QC subfunctions do not exclude voxels where mean is 0 (only where sd is 0)
• [FIX] fixed typo in error message of ciftify_clean_img
• [FIX] ciftify clean image forces na to zero when in covariates when doing confound regression
• [FIX] fixed the fmriprep workdir bug in the run script (it now does detect the workdir as writable)
• [ENC] cifitfy_recon_all can be called with the --resample-to-T1w32k after it completes - in this case it only does the last resampling_to_t1w_32k
• [FIX] fixed major error in resample to T1w 32k space (note: previous versions where leaving resampled surfaces in MNI space)
• [ENC] The docker run script now has a --rerun-if-incomplete that will delete failed or incomplete ciftify outputs and rerun them.
• [ENC] ciftify_recon_all can take a freesurfer license argument (--fs-license). Which makes it easier to run with singularity exec

v2.0.8

The first release ready for pip

v2.0.7

moved location of BIDS apps and some tests