Open cmaumet opened 4 months ago
cmaumet
commented
4 months ago This team has a corresponding file marked as "wip" and initially started by @elodiegermani (see https://github.com/Inria-Empenn/narps_open_pipelines/issues/3).
To be done: Verification of the adequation between textual description and code, correction of mistakes (if necessary)
bclenet
commented
2 months ago The code runs with PR #191 but remains to be (reviewed and) tested on a larger number of subjects. For now, the correlation results with 4 subjects : [0.37, 0.15, 0.37, 0.15, 0.14, 0.32, 0.14, 0.32, 0.00]
bclenet
commented
3 weeks ago Correlation results with commit 01c7ebd and 108 subjects : [0.50, 0.08, 0.50, 0.08, 0.59, 0.22, 0.59, 0.22, 0.04]
Softwares
"general.softwares": "FSL 5.0.4 and Feat v6 ",
Input data
derivatives (fMRIprep)
Additional context
$ narps_description -t 4TQ6 --json { "general.teamID": "4TQ6", "general.NV_collection_link": "https://neurovault.org/collections/4869/", "general.results_comments": "NA", "general.preregistered": "No", "general.link_preregistration_form": "NA", "general.regions_definition": "Using the Harvard-Oxford Atlas as a reference, alongside general anatomical knowledge.", "general.softwares": "FSL 5.0.4 and Feat v6 ", "exclusions.n_participants": "108", "exclusions.exclusions_details": "No exclusions", "preprocessing.used_fmriprep_data": "Yes", "preprocessing.preprocessing_order": "fmriprep v1.1.4 pre-processed data was used.", "preprocessing.brain_extraction": "fmriprep v1.1.4 was used: T1-weighted images were skull-stripped using antsBrainExtraction.sh (ANTs 2.2.0) and OASIS as target template. ", "preprocessing.segmentation": "fmriprep v1.1.4 was used: \"Brain tissue segmentation of cerebrospinal fluid (CSF), white-matter (WM) and gray-matter (GM) was performed on the brain-extracted T1w using fast (FSL 5.0.9, RRID:SCR_002823, Zhang, Brady, and Smith 2001)\"", "preprocessing.slice_time_correction": "NA ", "preprocessing.motion_correction": "fmriprep v1.1.4 was used: \"Head-motion parameters with respect to the BOLD reference (transformation matrices, and six corresponding rotation and translation parameters) are estimated before any spatiotemporal filtering using mcflirt (FSL 5.0.9, Jenkinson et al. 2002)", "preprocessing.motion": "6", "preprocessing.gradient_distortion_correction": "NA", "preprocessing.intra_subject_coreg": "NA", "preprocessing.distortion_correction": "NA", "preprocessing.inter_subject_reg": "fmriprep v1.1.4 was used: \"bbregister was used to generate transformations from EPI-space to T1w-space\"\u2002", "preprocessing.intensity_correction": "NA", "preprocessing.intensity_normalization": "NA ", "preprocessing.noise_removal": "NA", "preprocessing.volume_censoring": "NA", "preprocessing.spatial_smoothing": "6mm FWHM Gaussian kernel, applied to the fmriprep data, so in MNI space", "preprocessing.preprocessing_comments": "NA", "analysis.data_submitted_to_model": "108 participants, four scans each, all collected at the same scan visit/time point.", "analysis.spatial_region_modeled": "Full Brain", "analysis.independent_vars_first_level": "Event-Related design, 4 second events, with parametric modulation based on amount gained or lost on each trial. One 'gain' regressor, and one 'loss' regressor.\nFirst temporal derivatives of the two regressors were also used, along with temporal filtering (60 s) of all the independent variable time-series. \nNo motion parameter regressors used. ", "analysis.RT_modeling": "none", "analysis.movement_modeling": "0", "analysis.independent_vars_higher_level": "For second level analysis, a group level between-subjects analysis was run to compare between \"equal range\" and \"equal indifference\" groups; no additional covariates, no additional between-subject effects.\nFor the within-group effects a group average analysis was computed with a single, constant, regressor. Also no covariates in these analyses.", "analysis.model_type": "Mass Univariate.", "analysis.model_settings": "First level: Standard FSL approach, using FILM prewhitening for correction of autocorrelation and high-pass filtering (60 s) to remove low frequency effects from both the data, and the model.\nSecond level (single-subject, mean of all four scans) analyses: Fixed effects analysis.\nGroup level: Mixed effects \"FLAME 1\". Specific variance structure: As in FSL's FLAME-1 model. \n", "analysis.inference_contrast_effect": "First-level analyses: Linear contrast effects: 'Gain' vs. baseline, 'Loss' vs. baseline.\nSecond-level: Linear contrast effects - simple mean across each subjects four scans, for each lower-level contrast.\nGroup-level (group average) analysis: Simple mean across all subjects for each lower-level contrast. \nGroup-level (between-groups comparison): Linear effect between groups for each lower-level contrast.", "analysis.search_region": "Whole Brain", "analysis.statistic_type": "Cluster-wise: Threshold-free Cluster Enhancement (TFCE) with default parameters.", "analysis.pval_computation": "FSL's 'Randomise' non-parametric permutation testing algorithm was used for inference.", "analysis.multiple_testing_correction": "5000 permutations were run using 'Randomise'.", "analysis.comments_analysis": "NA", "general.general_comments": "NA", "categorized_for_analysis.region_definition_vmpfc": "atlas HOA", "categorized_for_analysis.region_definition_striatum": "atlas HOA", "categorized_for_analysis.region_definition_amygdala": "atlas HOA", "categorized_for_analysis.analysis_SW": "FSL", "categorized_for_analysis.analysis_SW_with_version": "FSL 5.0.4", "categorized_for_analysis.smoothing_coef": "6", "categorized_for_analysis.testing": "randomise", "categorized_for_analysis.testing_thresh": "", "categorized_for_analysis.correction_method": "TFCE", "categorized_for_analysis.correctionthresh": "p<0.05", "derived.n_participants": "108", "derived.excluded_participants": "n/a", "derived.func_fwhm": "6", "derived.con_fwhm": "", "comments.excluded_from_narps_analysis": "No", "comments.exclusion_comment": "Resampled image offset and too large compared to template.", "comments.reproducibility": "3", "comments.reproducibility_comment": "" }
List of tasks
Please tick the boxes below once the corresponding task is finished. :+1:
status: ready for devlabel to it.team_{team_id}.pyinside thenarps_open/pipelines/directory. You can use a file insidenarps_open/pipelines/templatesas a template if needed.tests/pipelines/test_team_*as examples.