Installation instructions for standalone fmriprep are out of date, causing crashes.

[bbfrederick]

We've recently updated our standalone fmriprep installation fmriprep 1.5.8 (and will now go to 20.0.x) from 1.4.1. We have found that AROMA processing crashes with the following error:

`
Node Name: fmriprep_wf.single_subject_017_wf.func_preproc_task_session3_wf.ica_aroma_wf.ica_aroma
File: /data/latncase/MDD_STRESS/fmriprep/test_ERISONE2/derivatives/fmriprep/sub-017/log/20200227-134551_1da3a78f-5ea2-4ce5-90ee-b7f94ab0e167/crash-20200228-001011-mai14-ica_aroma-2e188a62-9b80-471c-8dbc-0dfcb69d4583.txt
Working Directory: /data/latncase/MDD_STRESS/fmriprep/work/fmriprep_wf/single_subject_017_wf/func_preproc_task_session3_wf/ica_aroma_wf/ica_aroma
Inputs:

TR: 2.0
args: -np
compress_report: auto
denoise_type: nonaggr
dim:
environ: {}
feat_dir:
fnirt_warp_file:
in_file:
mask:
mat_file:
melodic_dir:
motion_parameters:
out_dir: out
out_report: ica_aroma_reportlet.svg
report_mask:
Traceback (most recent call last):
File "/PHShome/bbf2/software/anaconda3/envs/fmriprep158/lib/python3.7/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/PHShome/bbf2/software/anaconda3/envs/fmriprep158/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/PHShome/bbf2/software/anaconda3/envs/fmriprep158/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/PHShome/bbf2/software/anaconda3/envs/fmriprep158/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/PHShome/bbf2/software/anaconda3/envs/fmriprep158/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/PHShome/bbf2/software/anaconda3/envs/fmriprep158/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 792, in _run_interface
self.raise_exception(runtime)
File "/PHShome/bbf2/software/anaconda3/envs/fmriprep158/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 723, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
ICA_AROMA.py -tr 2.000 -np -den nonaggr -i /data/latncase/MDD_STRESS/fmriprep/work/fmriprep_wf/single_subject_017_wf/func_preproc_task_session3_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_smooth.nii.gz -m /data/latncase/MDD_STRESS/fmriprep/work/fmriprep_wf/single_subject_017_wf/func_preproc_task_session3_wf/bold_std_trans_wf/_key_MNI152NLin6Asym/mask_std_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz -meldir /data/latncase/MDD_STRESS/fmriprep/work/fmriprep_wf/single_subject_017_wf/func_preproc_task_session3_wf/ica_aroma_wf/melodic -mc /data/latncase/MDD_STRESS/fmriprep/work/fmriprep_wf/single_subject_017_wf/func_preproc_task_session3_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /data/latncase/MDD_STRESS/fmriprep/work/fmriprep_wf/single_subject_017_wf/func_preproc_task_session3_wf/ica_aroma_wf/ica_aroma/out
Standard output:

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

Standard error:
usage: ICA_AROMA.py [-h] -o OUTDIR [-i INFILE] [-mc MC] [-a AFFMAT] [-w WARP]
[-m MASK] [-f INFEAT] [-tr TR] [-den DENTYPE] [-md MELDIR]
[-dim DIM]
ICA_AROMA.py: error: unrecognized arguments: -np
Return code: 2
`
The '-np' option does not exist in ICA-AROMA-0.4.1beta (what is listed in the documentation).

This error does not occur on the containerized version of fmriprep. Comparing the Dockerfile to the documented requirements, it seems that:

1. ICA-AROMA-0.4.5 is the appropriate version.
2. bids-validator should be version 1.4.0, not 1.1.0.
3. c3d is no longer a dependency.

I've fixed a local copy of installation.rst (and an unrelated typo in CONTRIBUTING.md), and would be happy to do a pull request with the fix.

Blaise

[effigies]

@bbfrederick A PR would be most welcome. Thank you for working through this.

We've talked a couple times about trying to make ICA-AROMA a bit more friendly to install and use (basically put on PyPI), but none of us has had the bandwidth to take on another maintenance project.

[bbfrederick]

PR submitted.

You could make wget a prerequisite, then have a script that just fetches the appropriate precompiled binaries from wherever as an intermediate step. But yeah, somebody would have to write and test it.

I'm a complete convert to the containerized distribution. Unfortunately, I use two HPC's and one won't allow me to use it in singularity because of security concerns (Them: "We don't have the bandwidth to hand check every version of every container for malicious software." Me: "That's the whole point of singularity - it doesn't let me do anything I couldn't do already, so why would you have to check it?" Them: "Well, we don't know that. We have to do a careful examination of the issue and we don't have the bandwidth to do that either".) I opened a ticket to install it in July of 2019, and they're still "looking into it". Actually, they just closed my ticket, so I guess they aren't.

The second cluster would be fine with me installing it, except the entire cluster runs on Centos 6 (singularity needs Centos 7 minimum) and they have no timeline for upgrading (SMH).

So standalone it is for the time being.