Query for fMRIprep and MRIQC for T1w images is differnet

[jpurcel8]

Hello,
fMRIPrep looks for T1w images with the query get(suffix='T1w', dataype='anat'), while MRIQC appears to use a different mechanism. Can the MRIQC mechanism be set to the same one that fMRIPrep uses?
Thanks,

[oesteban]

Can you point me to the particular section of MRIQC code you think we could make more consistent with fMRIPrep?

[jpurcel8]

fMRIPrep looks for T1w images with the query get(suffix='T1w', dataype='anat'), while MRIQC appears to use a different mechanism. I don't know what this other mechanism is per se, but the consequence is that when I have non-standard T1w images, then MRIQC does not run. (e.g. T1w images that only slice through the hippocampus). While, of course, it runs fine with fMRIprep.
Thanks!

[mgxd]

The relevant bits are here:
https://github.com/poldracklab/mriqc/blob/5898396026817ce114bbc90bac0dd5d7c48618e0/mriqc/cli/parser.py#L449-L461

https://github.com/poldracklab/mriqc/blob/ee433f28d0c4d84eea2d050c54002ca823c86531/mriqc/utils/bids.py#L9-L32

but the consequence is that when I have non-standard T1w images, then MRIQC does not run.

@jpurcel8 could you share this T1w's filename, and what options you are passing in to MRIQC?

[jpurcel8]

Hello, *T1w filename: *sub-tpc000_ses-balt_acq-hippoc1_T1w.nii.gz * MRIQC options: * setenv SINGULARITYENV_TEMPLATEFLOW_HOME /home/jpurcel8/templateflow; singularity run --cleanenv /home/jpurcel8/mriqc_latest.simg /home/jpurcel8/TPC_Project/bids /home/jpurcel8/TPC_Project/fmriprep/mriqc participant --participant_label tpc000 --work-dir /home/jpurcel8/TPC_Project/work_directory -m T1w Thanks

…

On Thu, Oct 15, 2020 at 2:01 PM Mathias Goncalves ***@***.***> wrote: The relevant bits are here: https://github.com/poldracklab/mriqc/blob/5898396026817ce114bbc90bac0dd5d7c48618e0/mriqc/cli/parser.py#L449-L461 https://github.com/poldracklab/mriqc/blob/ee433f28d0c4d84eea2d050c54002ca823c86531/mriqc/utils/bids.py#L9-L32 but the consequence is that when I have non-standard T1w images, then MRIQC does not run. @jpurcel8 <https://github.com/jpurcel8> could you share this T1w's filename, and what options you are passing in to MRIQC? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#866 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKXGGELB63IT2WRQJEYHO7DSK42GRANCNFSM4SQ43BYA> .

-- Jeremy Purcell, PhD Faculty Research Scientist University of Maryland Biology/Psychology Building 0125D 4094 Campus Dr. College Park, MD 20742 Telephone: 517-282-5231 jpurcel8@umd.edu purcel14@gmail.com www.jjpurcell.com

[effigies]

Linking in the neurostars issue.

@jpurcel8 has some wonky T1w images in misc/*_T1w.nii.gz. fMRIPrep avoids these because we request datatype='anat', while MRIQC only queries for suffix.