[ENH] Include repetition time in functional summary

[wiheto]

Changes proposed in this pull request

Closes #1425. Small change that adds the repetition time to the functional reports.

(Was looking how the reports were generated and added it).

Documentation that should be reviewed

[welcome]

Thanks for opening this pull request! We have detected this is the first time for you to contribute to fMRIPrep. Please check out our contributing guidelines.
We invite you to list yourself as a fMRIPrep contributor, so if your name is not already mentioned, please modify the .zenodo.json file with your data right above Russ' entry. Example:

{
   "name": "Contributor, New FMRIPrep",
   "affiliation": "Department of fMRI prep'ing, Open Science Made-Up University",
   "orcid": "<your id>"
},
{
   "name": "Poldrack, Russell A.",
   "affiliation": "Department of Psychology, Stanford University",
   "orcid": "0000-0001-6755-0259"
},

Of course, if you want to opt-out this time there is no problem at all with adding your name later. You will be always welcome to add it in the future whenever you feel it should be listed.

[effigies]

Looks good. Some cleanups, though.

[effigies]

@wiheto I'm planning to release 1.3.1 today. Do you have time to finish this off?

[wiheto]

Can do. I can sit this morning and fix all the stuff you have suggested (here and niworkflows). I’ll get to it in a few hours.

…

14 feb. 2019 kl. 06:19 skrev Chris Markiewicz ***@***.***>: @wiheto I'm planning to release 1.3.1 today. Do you have time to finish this off? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[oesteban]

@effigies, why don't we release a 1.3.0-2? after all we needed to fix 1.3.0. That would also give @wiheto some extra time for these fixes (and release 1.3.1 asap).

[effigies]

Because we have an actual change in functionality (#1467) already in master.

[oesteban]

Yeah, I was going to slack you right now. I had that situation as well before releasing 1.3.0-1. Let me make a backport.

[effigies]

We have a patched Docker container people can use for now. I don't know that we need to rush beyond just getting it out today.

[oesteban]

It was just cherry-picking your commit based off 1.3.0.post1, it can't hurt. - https://github.com/poldracklab/fmriprep/releases/tag/1.3.0.post2

[wiheto]

Committed suggestions.

Also here is an example of the output of the changes (if making a tmp.tsv confounds file with the confounds a,b,c).

from fmriprep.interfaces.reports import FunctionalSummary
summary = FunctionalSummary(slice_timing=True,
                        registration='FreeSurfer',
                        registration_dof=6,
                        pe_direction='i',
                        tr=2,
                        distortion_correction='a string',
                        fallback=False,
                        output_spaces=['MNI152NLin2009cAsym'],
                        confounds_file='tmp.tsv')
summary.run()

Output file in ./reports.html is:

                <h3 class="elem-title">Summary</h3>
                <ul class="elem-desc">
                        <li>Repetition time (TR): 2s</li>
                        <li>Phase-encoding (PE) direction: Left-Right</li>
                        <li>Slice timing correction: Applied</li>
                        <li>Susceptibility distortion correction: a string</li>
                        <li>Registration: FreeSurfer <code>bbregister</code> (b$
                        <li>Functional series resampled to spaces: MNI152NLin20$
                        <li>Confounds collected: a, b, c</li>
                </ul>

The only thing I was a slight unsure about is if the flag Mandetory=True should be there. Is it always the case that RepetitionTime is in metadata?

[effigies]

The only thing I was a slight unsure about is if the flag Mandetory=True should be there. Is there always able to get RepetitionTime in metadata?

Yes. This is required by BIDS.

[wiheto]

Good, then this won't break anything.

[effigies]

LGTM!