What is new

0.1.1: News on the interface front.

Design matrices:

• Whereas previously you had to provide fmrifit with a formal description of the experimental design, you may now provide fmrifit with a custom design matrix. Have a look at the new command line function (CLF) csv2design.
• You would like to use FSL together with fmristats? You can now provide fmrifit with FSL’s own design matrix. Have a look at the new CLF fsl2design.
• You would like to use SPM together with fmristats? You can now provide fmrifit with SPM’s own design matrix. Have a look at the new CLF spm2design.

BOLD contrasts:

• You can now calculate any BOLD contrast post-hoc after fitting your model to the FMRI data. This means you don’t need to provide fmrifit with a fixed, a-priory defined list of BOLD contrasts any more.

• You can now also specify BOLD contrasts in the form of a named dictionary. This named dictionary can be re-use when analysing multible subjects. Have a look at the files:

  • If you are using FSL: fsl-parameter-dict.txt.
  • If you are using SPM: spm-parameter-dict.txt.

Head movements and reference spaces:

• The interface has grown and now gives you even more options. Have a look at fmririgids.
• You would like to use the head movement estimates as they were estimated by FSL? Have a look at the new fsl2rigids.
• You would like to use the head movement estimates as they were estimated by SPM? Have a look at the new spm2rigids.

Together, your analysis may now look as follows:

# Use the head movements as estimated by SPM
spm2rigids -v \
    --study-name abc --cohort run0 --id 0 --datetime 2019-01-22-1300 \
    --paradigm ckq
    --par rp_run0_5.txt \
    --par-path raw3/fmristats_01/run0/realign \

# Analyse your data in native space (the space isometric to the subject)
fmripop -v \
    --study-name abc --cohort run0 --id 0 --datetime 2019-01-22-1300 \
    --paradigm ckq
    --vb-name isospm \
    --rigids spm --diffeomorphism-nb identity --resolution 0. \

# Fit the data
fmrifit -v \
    --study-name abc --cohort run0 --id 0 --datetime 2019-01-22-1300 \
    --paradigm ckq \
    --vb-name isospm --diffeomorphism identity --rigids spm \
    --stimulus-block left --control-block right --fwhm 5 \
    --use-custom-design --design spm --parameter-dict spm-parameter-dict.txt

Last but not least, the in-line documentation has further been polished.

Everything new in 0.1.0: Well, not everything but well enough to justify a version increase.

• Most importantly, fmristats is a lot faster than before. You may now expect the calculations to be finished in around 4h.
• The API now consistently builds around the study instance that has been introduced in 0.0.4. This makes the whole user interface much more streamlined and, well, consistent. To get an idea of the changes, please have a look at the Getting to know fmristats and Analysing multiple subjects chapters.
• Last but not least, the documentation has been polished a lot.

Unfortunately, version 0.1.0 is not backwards compatible with versions <0.1.0. Please upgrade to the most recent version.