Fmriprep 1.4.1 ICA-AROMA failure

1

Hello - I am receiving a consistent failure during the ICA_AROMA step for all runs:

------------------------------- RUNNING ICA-AROMA ------------------------------- 
--------------- 'ICA-based Automatic Removal Of Motion Artifacts' --------------- 

Step 1) MELODIC
  - The existing/specified MELODIC directory will be used.
Step 2) Automatic classification of the components
  - registering the spatial maps to MNI
  - extracting the CSF & Edge fraction features
Standard error:
Image Exception : #22 :: ERROR: Could not open image /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
Traceback (most recent call last):
  File "/opt/ICA-AROMA/ICA_AROMA.py", line 202, in <module>
    edgeFract, csfFract = aromafunc.feature_spatial(fslDir, outDir, scriptDir, melIC_MNI)
  File "/opt/ICA-AROMA/ICA_AROMA_functions.py", line 363, in feature_spatial
    numICs = int(subprocess.getoutput('%sfslinfo %s | grep dim4 | head -n1 | awk \'{print $2}\'' % (fslDir, melIC) ))
ValueError: invalid literal for int() with base 10: 'ERROR: Could not open file'
Return code: 1

It seems as though this step is looking for a file that does not exist within the container:
/usr/share/fsl/5.0/data/standar/MNI152_T1_2mm_brain.
I have confirmed that this file does not exist through logging into the container using singularity shell.

The container was built using:
singularity build fmriprep-1.4.1.simg docker://poldracklab/fmriprep:1.4.1

Here is the fmriprep command I am using:

singularity run --cleanenv /data/containers/fmriprep-1.4.1.simg 
/scratch/dmoracze/rawdata $TMPDIR/out 
participant --participant_label sub-03 
-w $TMPDIR/wrk 
--fs-license-file /home/dmoracze/license.txt 
--output-spaces T1w func fsaverage6 MNI152NLin6Asym 
--longitudinal --use-aroma --error-on-aroma-warnings

Any thoughts as to why this is failing? I previously ran this same command with no issues, but I forgot to add T1w to --output-spaces so I am rerunning to include this space.

Thanks for your help!

2

Hi @dmoracze, the FSL MNI template is missing in fMRIPrep 1.4.1.

If there is not reason preventing you from upgrading to 1.5.0, that will do. Otherwise, let me know and I can help you workaround this.

3

Thanks for the response, @oesteban. I did notice that the files are included in 1.5.0, but this version is also causing me issues. The same fmriprep command above fails immediately (subbing fmriprep-1.5.0 in place of fmriprep-1.4.1).

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 311, in main
    opts = get_parser().parse_args()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 284, in get_parser
    latest = check_latest()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/version.py", line 22, in check_latest
    cachefile.parent.mkdir(parents=True, exist_ok=True)
  File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1241, in mkdir
    self._accessor.mkdir(self, mode)
OSError: [Errno 30] Read-only file system: '/home/fmriprep/.cache/fmriprep'
/spin1/swarm/dmoracze/PEvgcUGFWf/cmd.0: line 1:  STATUS=1: command not found
4

Please check out this thread from here: https://github.com/poldracklab/fmriprep/issues/1778#issuecomment-531884251