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[FIX,DOC] change ica-aroma filenames to fit current naming scheme #1861

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Nov 6, 2019
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[FIX,DOC] change ica-aroma filenames to fit current naming scheme #1861

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12 changes: 6 additions & 6 deletions docs/workflows.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -591,18 +591,18 @@ regressors (a separate GLM with both noise and signal regressors needs to be use
Therefore instead of regressors, *fMRIPrep* produces *non*-aggressive denoised 4D NIFTI
files in the MNI space:

``*bold_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_brainmask.nii.gz``
``*space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz``

Additionally, the MELODIC mix and noise component indices will
be generated, so non-aggressive denoising can be manually performed in the T1w space with ``fsl_regfilt``, *e.g.*::

fsl_regfilt -i sub-<subject_label>_task-<task_id>_bold_space-T1w_preproc.nii.gz \
-f $(cat sub-<subject_label>_task-<task_id>_bold_AROMAnoiseICs.csv) \
-d sub-<subject_label>_task-<task_id>_bold_MELODICmix.tsv \
-o sub-<subject_label>_task-<task_id>_bold_space-<space>_AromaNonAggressiveDenoised.nii.gz
fsl_regfilt -i sub-<subject_label>_task-<task_id>_space-T1w_desc-preproc_bold.nii.gz \
-f $(cat sub-<subject_label>_task-<task_id>_AROMAnoiseICs.csv) \
-d sub-<subject_label>_task-<task_id>_desc-MELODIC_mixing.tsv \
-o sub-<subject_label>_task-<task_id>_space-T1w_desc-AROMAnonaggr_bold.nii.gz

*Note*: The non-steady state volumes are removed for the determination of components in melodic.
Therefore ``*MELODICmix.tsv`` may have zero padded rows to account for the volumes not used in
Therefore ``*MELODIC_mixing.tsv`` may have zero padded rows to account for the volumes not used in
melodic's estimation of components.

A visualization of the AROMA component classification is also included in the HTML reports.
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