cmaumet
commented
8 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)
Softwares
"SPM 7487"
Input data
raw data
Additional context
$ narps_description -t 0I4U --json { "general.teamID": "0I4U", "general.NV_collection_link": "https://neurovault.org/collections/4938/", "general.results_comments": "NA", "general.preregistered": "No", "general.link_preregistration_form": "NA", "general.regions_definition": "vmPFC was defined based on the following bilateral region from Harvard Oxford atlas:\n25 Frontal medial cortex\nAmygdala was defined using based on Neuromorphometrics atlas regions:\n31 Right Amygdala\n32 Left Amygdala\nVentral striatum was defined based on Neuromorphometrics atlas regions:\n 23 and 30 - Left and right accumbens ", "general.softwares": "SPM 7487", "exclusions.n_participants": "108", "exclusions.exclusions_details": "NA", "preprocessing.used_fmriprep_data": "No", "preprocessing.preprocessing_order": "All Pre-processing steps were performed using SPM12\n1. Realign (to first) and unwarp using provided fieldmap (vdm5 computed)\n2. Co-registration to structural scan\n3. Segmentation and spatial normalization of structural data to MNI space using Segment function\n4. Application of the normalization parameters (iy) from step 3 to the co-registered functional data\n5. Masking of non-grey matter voxels in normalized functional data using binary downsampled wc1 images (>0.2 threshold)\n6. Smoothing with Gaussian kernel of 5 mm FWHM ", "preprocessing.brain_extraction": "NA", "preprocessing.segmentation": "Segmentation function in SPM12", "preprocessing.slice_time_correction": "Not performed", "preprocessing.motion_correction": "Default realign and unwarp in SPM12 including fieldmap based distortion correction:\nRigid body\nRegister to first\n4th Degree B-Spline", "preprocessing.motion": "", "preprocessing.gradient_distortion_correction": "s.above", "preprocessing.intra_subject_coreg": "NA", "preprocessing.distortion_correction": "Distortion correction as integrated in realign- and unwarp in SPM12 using default parameters including a precomputed phase map", "preprocessing.inter_subject_reg": " - SPM12:\n- volume based registration to MNI space using normalization parameters (iy) derived from T1 scan using Segment function (default paramters) in SPM12 (comprises distortion correction)\n- final resolution is 1.5 mm isotropic ", "preprocessing.intensity_correction": "Bias correction for T1 as default in the SPM12 segment utility", "preprocessing.intensity_normalization": "Default scaling in SPM (\"session specific grand mean scaling\")", "preprocessing.noise_removal": "6 motion parameters were included into the first level analyses", "preprocessing.volume_censoring": "No censoring applied", "preprocessing.spatial_smoothing": "Smoothing using a Gaussian kernel of 5 mm FWHM (Smooth function in SPM)", "preprocessing.preprocessing_comments": "NA", "analysis.data_submitted_to_model": "No subjects or time poins excluded (all 4 sessions each 453 frames for all 108 subjects used)", "analysis.spatial_region_modeled": "Analyses were restricted to a grey matter mask extracted from another dataset to exclude white matter regions from analyses", "analysis.independent_vars_first_level": "All in SPM12: \nEvent-related design, 4 within subject sessions\n1 Condition: Stimulus presentation, onsets based on tsv file, duration 4 seconds\n2 Parametric modulators: Gain and loss modelled with 1st order polynomial expansion\n1 Condition: button press, onsets based on tsv file, duration 0 seconds\nStandard 6 motion parameters included as regressors per session\nHRF: Canonical plus temporal derivative\nExplicit grey matter mask applied, No other masking thresholds\nSerial correlation: AR(1)\nAll other parameters as default\n2 T-contrasts generated modelling positive effect of gain and loss per subject across all sessions", "analysis.RT_modeling": "onset", "analysis.movement_modeling": "1", "analysis.independent_vars_higher_level": "Separate one sample t-tests for gain, loss for each group (equal Ind, equal Range) including age and sex as covariates to test for parametric effects of gain and loss in each group (Hypotheses 1-8)\nTwo-sample t-tests (with age and sex as covariates) to compare equal Range vs equal Indifference (Hypothesis 9) ", "analysis.model_type": "Mass Univariate", "analysis.model_settings": "For 1st level s. above.\nFor 2nd level:\nRandom effect SPM default second level (one-sample t-tests for hypotheses 1-8 and two-sample t-test for hypothesis 9), age and sex included as covariates\nUnequal variance between groups assumed ", "analysis.inference_contrast_effect": "1st level: two t-contrast contrasts generated: positive effect of gain and positive effect of loss per subject across all sessions)\n2nd level: first level con maps entered into 2nd level. According to the respective hypothesis t-contrast for positive or negative effect of gain loss (hypotheses 1-8) or t-contrast for group comparison (hypothesis 9)\nWhole brain FWE correction performed on voxel-level for all 2nd level analyses. Masks described above were applied to test for whole-brain significant effects in specified regions as based on the hypotheses ", "analysis.search_region": "Whole-brain corrected p-value threshold applied testing for significant effects within the specified regional masks", "analysis.statistic_type": "Voxel-wise whole-brain FWE corrected as in SPM", "analysis.pval_computation": "NA", "analysis.multiple_testing_correction": "FWE (Random field Theory)", "analysis.comments_analysis": "NA", "general.general_comments": "NA", "categorized_for_analysis.region_definition_vmpfc": "atlas HOA", "categorized_for_analysis.region_definition_striatum": "atlas Neuromorphometrics", "categorized_for_analysis.region_definition_amygdala": "atlas Neuromorphometrics", "categorized_for_analysis.analysis_SW": "SPM", "categorized_for_analysis.analysis_SW_with_version": "SPM12", "categorized_for_analysis.smoothing_coef": "5", "categorized_for_analysis.testing": "parametric", "categorized_for_analysis.testing_thresh": "", "categorized_for_analysis.correction_method": "GRTFWE voxelwise", "categorized_for_analysis.correctionthresh": "", "derived.n_participants": "108", "derived.excluded_participants": "n/a", "derived.func_fwhm": "5", "derived.con_fwhm": "", "comments.excluded_from_narps_analysis": "No", "comments.exclusion_comment": "N/A", "comments.reproducibility": "2", "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.