[L3V8] Pipeline reproduction (SPM, raw)

[mselimata]

Softwares

SPM 12(v6906), Matlab 2017b

Input data

raw data

Additional contex

{
"general.teamID": "L3V8",
"general.NV_collection_link": "https://neurovault.org/collections/4888/",
"general.results_comments": "We analyzed the data as an confirmative study, no exploration was done.",
"general.preregistered": "No",
"general.link_preregistration_form": "NA",
"general.regions_definition": "In our analysis, the vmPFC was defined as a box ([20mm x 16mm x 16mm]) centered at the mid-centered (x-coordinate set to zero) peak coordinate reported in Tom et al (2007) ([0 39.3 -8.4]). The ventral striatum and the amygdala were defined based on the Oxford-Harvard atlas for subcortical regions, thresholded at 25% tissue probability. The bilateral nucleus accumbens was used as ventral striatum mask.",
"general.softwares": "SPM 12(v6906) on matlab 2017b",
"exclusions.n_participants": "101",
"exclusions.exclusions_details": "The following participants were excluded: sub-016, sub-018, sub-026, sub-030, sub-032, sub-116, and sub-120.\nThese participants were excluded based on severe head movement. Participants showing head displacements of >3 mm or >2 degrees were excluded. Head displacements were calculated from the realignment parameters. ",
"preprocessing.used_fmriprep_data": "No",
"preprocessing.preprocessing_order": "Realignment, co-registration, segmentation, normalization, smooth (6 mm).",
"preprocessing.brain_extraction": "Not performed.",
"preprocessing.segmentation": "Using the default segmentation function implemented in SPM 12. ",
"preprocessing.slice_time_correction": "Not performed.",
"preprocessing.motion_correction": "Software/method: SPM/Realignment (Est & Res), no fieldmap applied.\nReference scan: 1st scan.\nImage similarity: mutual information.\nInterpolation type: B-Spline (4th degree). Image transfomrations were combined with normalization.\nNo slice-to-volume registration.",
"preprocessing.motion": "",
"preprocessing.gradient_distortion_correction": "Not performed.",
"preprocessing.intra_subject_coreg": "Software/method: SPM 12/Coregister: Estimate. Using the mean image of re-aligned images as reference, T1w image as the source image. \nType of transofrmation: rigid-body transformation.\nCost function: Normalised Mutual Information.\nInterpolation method: NA ",
"preprocessing.distortion_correction": "No",
"preprocessing.inter_subject_reg": "Software/method: SPM/Normalization: Write.\nVolume based registration was used.\nImage type registered: T1.\nPreprocessing to images: Unified segmentation, included the bias field correction.\nTemplate space: MNI, SPM Tissue Probabiltiy Map (TPM.nii), resolution [1.5 1.5 1.5] mm^3.\nAdditional template tranformation for reporting: not used.\nChoice of warp: nonlinear stationary velocity field (deformation field).\nUsef of regularization: yes, default value from SPM ([0 .001 0.5 0.05 0.2]).",
"preprocessing.intensity_correction": "Yes, built-in unified segmentation.",
"preprocessing.intensity_normalization": "Yes, we used the default value. i.e., session regressor.",
"preprocessing.noise_removal": "Not applied.",
"preprocessing.volume_censoring": "Not applied.",
"preprocessing.spatial_smoothing": "Software/Method: SPM 12/Smooth,\nSize and type of smoothing kernel: 3D Gaussian kernel, with FWHM [6mm 6mm 6mm].\nSpace: MNI volume.",
"preprocessing.preprocessing_comments": "No",
"analysis.data_submitted_to_model": "All time points form 101 participants.",
"analysis.spatial_region_modeled": "Whole-brain.",
"analysis.independent_vars_first_level": "Event-related design was used. Onset of each trial, duration = 0 (impulse response function). Each trial was associated with two parametric modulators: (1) value of gain, (2) value of loss, each modeled as a linear function.\nHRF basis, Canonical only;\nDrift Regressors: SPM built-in cosine functions.\nMovement regressors: None;\nOther nuisance regressors: None\nOrthogonalization of regressors: the parametric modulators (gain, loss) are orthogonalized with respect to the main trial regressor and each other.\nUPDATE: Given the feedback from NARPS team, we found that the default value implicit mask implemented in SPM (spm.stats.fmr_spec.mthresh) resulted a small mask. We changed the value from 0.8 to 0.3. This doesn't change our conclusions. ",
"analysis.RT_modeling": "none",
"analysis.movement_modeling": "0",
"analysis.independent_vars_higher_level": "We used 5 independent 2nd models: (1) equal indifference with gain; (2) equal range with gain; (3) equal indifference with loss; (4) equal range with loss; (5) group effect model with loss. All models were built using SPM's flexible factorial design, with runs as within-subject factor (equal variance), and subject as between-subject factor (equal variance). For model 5, there is an additional factor of the group as the between-subject factor (equal variance). \nFor model 1-4, we tested the main effect of runs. For model 5, we tested the interaction between runs and groups.\nNo other covariates were included.",
"analysis.model_type": " Mass Univariate.",
"analysis.model_settings": "Random effect model: ordinary least squares in SPM.\nAutocorrelation model: FAST in SPM.\nIn our group model (model 5), we assumed equal variance between groups.",
"analysis.inference_contrast_effect": "In our model 1, we used the contrast [1 1 1 1] to get the average positive activation of the parametric modulator (gain value) across four runs.\nIn model 2, we used the contrast [1 1 1 1] to get the average positive activation of the parametric modulator (gain value) across four runs.\nIn model 3, we used the contrast [-1 -1 -1 -1] to get the average negative activation of the parametric modulator (loss value) across four runs. We used contrast [1 1 1 1] to get the average positive effect of the parametric modulator (loss value) across four runs.\nIn model 4, we used the contrast [-1 -1 -1 -1] to get the average negative activation of the parametric modulator (loss value) across four runs. We used contrast [1 1 1 1] to get the average positive effect of the parametric modulator (loss value) across four runs. \nIn model 5, we used the contrast[-1 1 -1 1 -1 1 -1 1] to get the group differences between equal indifference group and equal range group on the positive response to the losses. ",
"analysis.search_region": "we used the whole-brain cluster-level FWE correction (p < 0.05), based on uncorrected cluster forming threshold (p = 0.001). \nFor anatomical labelling, we used Harvard-Oxford Atlas ",
"analysis.statistic_type": "we used the whole-brain cluster-level FWE correction (p < 0.05), based on uncorrected cluster forming threshold (p = 0.001). ",
"analysis.pval_computation": "We used the standard parametric inference.",
"analysis.multiple_testing_correction": "For whole-brain corrected analysis, we used the whole-brain cluster-level FWE correction based on random field theory. ",
"analysis.comments_analysis": "NA",
"general.general_comments": "No",
"categorized_for_analysis.region_definition_vmpfc": "Other",
"categorized_for_analysis.region_definition_striatum": "atlas HOA",
"categorized_for_analysis.region_definition_amygdala": "atlas HOA",
"categorized_for_analysis.analysis_SW": "SPM",
"categorized_for_analysis.analysis_SW_with_version": "SPM12",
"categorized_for_analysis.smoothing_coef": "6",
"categorized_for_analysis.testing": "parametric",
"categorized_for_analysis.testing_thresh": "p<0.001",
"categorized_for_analysis.correction_method": "GRTFWE cluster",
"categorized_for_analysis.correction_thresh_": "p<0.05",
"derived.n_participants": "101",
"derived.excluded_participants": "016, 018, 026, 030, 032, 116, 120",
"derived.func_fwhm": "6",
"derived.con_fwhm": "",
"comments.excluded_from_narps_analysis": "No",
"comments.exclusion_comment": "Rejected due to large amount of missing brain in center.",
"comments.reproducibility": "2",
"comments.reproducibility_comment": ""
}

List of tasks

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