Open bclenet opened 1 year ago
During the NARPS study, Botvinik-Nezer performed a rectification (see : https://github.com/poldrack/narps/blob/master/ImageAnalyses/original_notebooks/PrepareMaps.ipynb) in which statistical maps for hypotheses 5 and 6 were multiplied by -1 for this reason:
Negative values in the images represent negative activation
After applying this rectification to the 2T6S neurovault correction, and with the current version of the code (PR #75 , commit e56bb63) we get the following correlation coefficients for hypotheses 1 to 9 (with 20 subjects) : [0.63, 0.51, 0.63, 0.51, -0.62, 0.57, 0.62, -0.57, 0.45].
Therefore, the code will now return the following files, so the correlation values are all positive :
l2_analysis_equalIndifference_nsub_{nb_sub}/_contrast_id_0003/_threshold0/spmT_0001_thr.nii
l2_analysis_equalIndifference_nsub_{nb_sub}/_contrast_id_0003/spmT_0001.nii
l2_analysis_equalRange_nsub_{nb_sub}/_contrast_id_0003/_threshold1/spmT_0002_thr.nii
l2_analysis_equalRange_nsub_{nb_sub}/_contrast_id_0003/spmT_0002.nii
The reasons for this issue are something we need to further understand.
Softwares
SPM
Input data
derivatives (fMRIprep)
Additional context
Pipeline reproduction is almost done, only one issue remains.
For the hypotheses 5 and 7, correlations values between reproduced maps and results are below zero (~= -0.99). The reason for that is that the team provided statistical maps in which negative values represent negative activation, although the opposite was expected in the NARPS study.
Therefore, results were modified before analysis. We need to do the same for the project. Changes need to be done on the results (
narps_open.data.results
) instead of in the pipeline code.Here is the description of the 2T6S results in their neurovault collection.
SPM{T_[53.0]} - contrast 1: Gamble_Loss
SPM{T_[53.0]} - contrast 2: - (Gamble_Loss)
SPM{T_[53.0]} - contrast 2: - (Gamble_Loss)
SPM{T_[53.0]} - contrast 1: Gamble_Loss
Here are the value ranges in the images:
[-2.92893, 0.97576]
[-0.70500, 2.22962]
[-0.97576, 2.92893]
[-2.22962, 0.70501]