MRIQC on T1w images error

[n2parker]

Hello, I have downloaded mriqc on a server using python3 with the work-around provided here https://github.com/poldracklab/mriqc/issues/470. The server does not have docker so the python installation was necessary. There are roughly 400 T1w MRI scans (nifty, .nii.gz) and structured in BIDS format. When I try to run "mriqc bids-root/ bids-outfolder/ participant" I get the following error: TypeError: not enough arguments for format string. Am I missing additional tags or commands? or is there some other issue?

[chrisgorgo]

Could you provide full console output (in addition to just the error line)?

[n2parker]

Hi, here is the full read out:

(mriqc) (Python3_env) [nparker@gpc-f102n084-ib0 nparker]$ mriqc /scratch/t/tpaus/nparker/Brazil_Wave2_Jan312016/Brazil_Wav2/All_Participants_Brazil_wave2/mri /scratch/t/tpaus/nparker/MRIQC/Brazil_Wave2_QC participant /home/t/tpaus/nparker/.conda/envs/mriqc/lib/python3.6/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters 2018-01-22 11:09:20,033 interface:WARNING FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI 2018-01-22 11:09:20,288 interface:WARNING FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI 2018-01-22 11:09:20,329 interface:WARNING FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI Traceback (most recent call last): File "/home/t/tpaus/nparker/.conda/envs/mriqc/bin/mriqc", line 11, in load_entry_point('mriqc==0.10.1', 'console_scripts', 'mriqc')() File "/home/t/tpaus/nparker/.conda/envs/mriqc/lib/python3.6/site-packages/mriqc/bin/mriqc_run.py", line 301, in main wf_list.append(build_workflow(dataset[mod], mod, settings=settings)) File "/home/t/tpaus/nparker/.conda/envs/mriqc/lib/python3.6/site-packages/mriqc/workflows/core.py", line 25, in build_workflow workflow = anat_qc_workflow(dataset, mod='T1w', settings=settings) File "/home/t/tpaus/nparker/.conda/envs/mriqc/lib/python3.6/site-packages/mriqc/workflows/anatomical.py", line 104, in anat_qc_workflow iqmswf = compute_iqms(settings, modality=mod) File "/home/t/tpaus/nparker/.conda/envs/mriqc/lib/python3.6/site-packages/mriqc/workflows/anatomical.py", line 245, in compute_iqms fwhm_interface = get_fwhmx() File "/home/t/tpaus/nparker/.conda/envs/mriqc/lib/python3.6/site-packages/mriqc/workflows/utils.py", line 169, in get_fwhmx afni_version = StrictVersion('%s.%s.%s' % afni.Info.version()) TypeError: not enough arguments for format string

[chrisgorgo]

Seems like AFNI compatibility issue. Please try updating AFNI or (even better) switch to using Docker or Singularity.

[n2parker]

Our server has Singularity however, I have never used this before. What are the steps to install the MRIQC container using Singularity? How do the commands to run the program differ from Docker?

[chrisgorgo]

Steps are similar to FMRIPREP. See http://fmriprep.readthedocs.io/en/latest/installation.html#singularity-container

[oesteban]

Hi @n2parker, did you finally solve this problem?

[n2parker]

Hi, yes this issue has been solved and I've successfully installed MRIQC. Thank you.