From 205822be2a5eb7402650223e34b7abc42752ed97 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 14 Aug 2024 12:22:58 +0200 Subject: [PATCH 1/3] fix: update FMRIPREP_VALID_NAMES if spike is allowed in fMRIPrepConfoundRemover --- junifer/preprocess/confounds/fmriprep_confound_remover.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/junifer/preprocess/confounds/fmriprep_confound_remover.py b/junifer/preprocess/confounds/fmriprep_confound_remover.py index 7a13abf61..0edc9766c 100644 --- a/junifer/preprocess/confounds/fmriprep_confound_remover.py +++ b/junifer/preprocess/confounds/fmriprep_confound_remover.py @@ -353,6 +353,9 @@ class fMRIPrepConfoundRemover(BasePreprocessor): "Check if this file is really an fmriprep confounds file. " "You can also deactivate spike (set spike = None)." ) + # NOTE: Check with @fraimondo about the spike mapping intent + # Add spike_name to FMRIPREP_VALID_NAMES + FMRIPREP_VALID_NAMES.append(spike_name) out = to_select, squares_to_compute, derivatives_to_compute, spike_name return out -- 2.52.0 From c273009e618b667966cdd0657e90bc38e03bf00f Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 14 Aug 2024 13:55:45 +0200 Subject: [PATCH 2/3] fix: hardcode spike mapping addition to module level for fMRIPrepConfoundRemover --- junifer/preprocess/confounds/fmriprep_confound_remover.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/junifer/preprocess/confounds/fmriprep_confound_remover.py b/junifer/preprocess/confounds/fmriprep_confound_remover.py index 0edc9766c..3a0f0859a 100644 --- a/junifer/preprocess/confounds/fmriprep_confound_remover.py +++ b/junifer/preprocess/confounds/fmriprep_confound_remover.py @@ -93,6 +93,9 @@ FMRIPREP_VALID_NAMES = [ for t_list in x.values() for elem in t_list ] +# NOTE: Check with @fraimondo about the spike mapping intent +# Add spike_name to FMRIPREP_VALID_NAMES +FMRIPREP_VALID_NAMES.append("framewise_displacement") @register_preprocessor @@ -353,9 +356,6 @@ class fMRIPrepConfoundRemover(BasePreprocessor): "Check if this file is really an fmriprep confounds file. " "You can also deactivate spike (set spike = None)." ) - # NOTE: Check with @fraimondo about the spike mapping intent - # Add spike_name to FMRIPREP_VALID_NAMES - FMRIPREP_VALID_NAMES.append(spike_name) out = to_select, squares_to_compute, derivatives_to_compute, spike_name return out -- 2.52.0 From 23bdc089cabfff24b99d9dc7183f3f86a2206638 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 14 Aug 2024 14:19:28 +0200 Subject: [PATCH 3/3] chore: add changelog 360.bugfix --- docs/changes/newsfragments/360.bugfix | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/changes/newsfragments/360.bugfix diff --git a/docs/changes/newsfragments/360.bugfix b/docs/changes/newsfragments/360.bugfix new file mode 100644 index 000000000..d02de688f --- /dev/null +++ b/docs/changes/newsfragments/360.bugfix @@ -0,0 +1 @@ +Enable ``spike`` mapping from ``adhoc`` to ``fmriprep`` for :class:`.fMRIPrepConfoundRemover` by `Leonard Sasse`_ and `Synchon Mandal`_ -- 2.52.0