--use-aroma fmriprep v24.0.0

Aref_Pariz · June 26, 2024, 3:31pm

Summary of what happened:

Hi all,
Is there any alternative flag(s) for *–use-aroma * flag in fmriprep v24.0.0? It looks like it is not supported anymore and I’m wondering what alternative flag may give me the same result as --use-aroma was giving.
Thanks,

FYI: I’m new in the realm of fMRI. So I would appreciate it if to give me more details

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep-docker  /Nifti derivatives participant --participant-label sub-01 --fs-license-file freesurfer_license.txt --output-spaces MNI152NLin6Asym -w work/ --use-aroma

Version:

fmriprep v24.0.0

tsalo · June 26, 2024, 3:42pm

There is no flag to run AROMA in fMRIPrep v24.0.0. ICA-AROMA is something that doesn’t need to be integrated into a minimal preprocessing pipeline, so the fMRIPrep devs consider it out of scope. A few of us have been working on implementing the ICA-AROMA pipeline on fMRIPrep derivatives in nipreps/fmripost-aroma, but that’s still a ways from being usable. In the meantime, you can probably run maartenmennes/ICA-AROMA directly.

jsein · June 26, 2024, 3:46pm

For history, aroma was removed from fmrirep since v23.1:

github.com/nipreps/fmriprep

Remove ICA-AROMA

opened 03:15PM - 17 Jan 23 UTC

closed 11:52AM - 09 Jun 23 UTC

effigies

feature

### What would you like to see added in fMRIPrep? ICA-AROMA is unmaintained, an…d appears to be incompatible with the version of MELODIC released in FSL 6.0.6.2. ``` Cmdline: ICA_AROMA.py -tr 2.000 -np -den nonaggr -i /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/smooth/vol0000_xform-00000_clipped_merged_smooth.nii.gz -m /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/vol0000_unwarped_merged_valid_average_corrected_brain_mask_maths_trans.nii.gz -meldir /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/melodic -mc /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out Stdout: ------------------------------- 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 Stderr: Image Exception : #21 :: Invalid ROI dimensions Invalid ROI dimensions Image Exception : #21 :: Invalid ROI dimensions Invalid ROI dimensions Image Exception : #63 :: No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat???? terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat???? Aborted (core dumped) rm: cannot remove '/scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat????.nii.gz': No such file or directory Image Exception : #63 :: No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr Aborted (core dumped) Traceback (most recent call last): File "/opt/ICA-AROMA/ICA_AROMA.py", line 210, in <module> aromafunc.register2MNI(fslDir, melIC, melIC_MNI, affmat, warp) File "/opt/ICA-AROMA/ICA_AROMA_functions.py", line 161, in register2MNI pixdim1 = float(subprocess.getoutput('%sfslinfo %s | grep pixdim1 | awk \'{print $2}\'' % (fslDir, inFile))) ValueError: could not convert string to float: 'Image Exception : #63 :: No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr\nNo image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr' Traceback: Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs setattr(outputs, key, val) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'nonaggr_denoised_file' trait of a _ICA_AROMAOutputSpecRPT instance must be a pathlike object or string representing an existing file, but a value of '/scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/denoised_func_data_nonaggr.nii.gz' <class 'str'> was specified. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 399, in run runtime = self._post_run_hook(runtime) File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/reportlets/segmentation.py", line 231, in _post_run_hook outputs = self.aggregate_outputs(runtime=runtime) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs raise FileNotFoundError(msg) FileNotFoundError: No such file or directory '/scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/denoised_func_data_nonaggr.nii.gz' for output 'nonaggr_denoised_file' of a ICA_AROMARPT interface ``` Given that people can request outputs in MNI152NLin6Asym space, it should be possible to run the necessary steps post-preprocessing, and then we will not have our hands tied by unmaintained dependencies. cc @jdkent ### Do you have any interest in helping implement the feature? Yes ### Additional information / screenshots _No response_

github.com/nipreps/fmriprep

AROMA not running in 23.1

opened 04:36PM - 15 Jun 23 UTC

closed 12:47PM - 17 Jun 23 UTC

dmd

bug

### What happened? In 23.1.1, but not 23.0.2, AROMA seems to not run - but does…n't error out, it just behaves as if it hadn't been specified. ### What command did you use? ```shell fMRIPrep version: 23.1.0 fMRIPrep command: /opt/conda/envs/fmriprep/bin/fmriprep /data/belleau_lab/TeenStress/E13347949 /data/belleau_lab/TeenStress/E13347949/derivatives participant --fs-license-file /cm/shared/freesurfer-license.txt --participant_label TS049 --output-spaces MNI152NLin6Asym:res-2 anat fsaverage --n_cpus 4 --mem-mb 16384 --notrack --dummy-scans 0 --use-aroma --use-syn-sdc --return-all-components -vv -w /data/fmriprep-workdir/ebelleau ``` ### What version of fMRIPrep are you running? 23.1.0 ### How are you running fMRIPrep? Singularity ### Is your data BIDS valid? Yes ### Are you reusing any previously computed results? No ### Please copy and paste any relevant log output. ```shell Here's the config it thinks it is starting with: 230614-14:08:46,994 nipype.workflow VERBOSE: fMRIPrep config: [environment] cpu_count = 32 exec_env = "singularity" free_mem = 181.0 overcommit_policy = "heuristic" overcommit_limit = "50%" nipype_version = "1.8.6" templateflow_version = "23.0.0" version = "23.1.1" [execution] bids_dir = "/data/belleau_lab/TeenStress/E13347949" bids_database_dir = "/data/fmriprep-workdir/ebelleau/20230614-140803_28b768a4-3108-471a-9419-6f55a68a6902/bids_db" bids_description_hash = "ecd58287c7e5111e4a4854c43e4d094e0bc8c59d52e1a549f4f5761fbb15bd7a" boilerplate_only = false sloppy = false debug = [] fmriprep_dir = "/data/belleau_lab/TeenStress/E13347949/derivatives" fs_license_file = "/cm/shared/freesurfer-license.txt" fs_subjects_dir = "/data/belleau_lab/TeenStress/E13347949/derivatives/sourcedata/freesurfer" layout = "BIDS Layout: ...lleau_lab/TeenStress/E13347949 | Subjects: 1 | Sessions: 0 | Runs: 4" log_dir = "/data/belleau_lab/TeenStress/E13347949/derivatives/logs" log_level = 15 low_mem = false md_only_boilerplate = false notrack = true track_carbon = false country_code = "CAN" output_dir = "/data/belleau_lab/TeenStress/E13347949/derivatives" me_output_echos = false output_layout = "bids" output_spaces = "MNI152NLin6Asym:res-2 anat fsaverage:den-164k" reports_only = false run_uuid = "20230614-140803_28b768a4-3108-471a-9419-6f55a68a6902" participant_label = [ "TS028",] templateflow_home = "/home/fmriprep/.cache/templateflow" work_dir = "/data/fmriprep-workdir/ebelleau" write_graph = false [workflow] anat_only = false aroma_err_on_warn = false aroma_melodic_dim = 0 bold2t1w_dof = 6 bold2t1w_init = "register" cifti_output = false dummy_scans = 0 fmap_bspline = false force_syn = false hires = true ignore = [] longitudinal = false medial_surface_nan = false project_goodvoxels = false regressors_all_comps = true regressors_dvars_th = 1.5 regressors_fd_th = 0.5 run_reconall = true skull_strip_fixed_seed = false skull_strip_template = "OASIS30ANTs" skull_strip_t1w = "force" slice_time_ref = 0.5 spaces = "MNI152NLin6Asym:res-2 anat fsaverage:den-164k MNI152NLin2009cAsym" use_aroma = true use_syn_sdc = "error" me_t2s_fit_method = "curvefit" [nipype] crashfile_format = "txt" get_linked_libs = false memory_gb = 16.384 nprocs = 4 omp_nthreads = 3 plugin = "MultiProc" resource_monitor = false stop_on_first_crash = false [seeds] master = 34084 ants = 46217 numpy = 28513 [nipype.plugin_args] maxtasksperchild = 1 raise_insufficient = false ``` ### Additional information / screenshots There are no errors in the html output. But when we run this with 23.0.2 with the exact same flags, we get AROMA output... when we run it with 23.1.1, we don't.