Hi, I ran mriqc on some t1 and resting state data (we have a sample of 160 children) with the aim to perform QC before running fmriprep and exclude subjects with artefacts and motion above a certain threshold. I changed the FD threshold to 0.5 and I now would like to exclude all the subjects that have more than 20% scan above this threshold. I have looked at the group plot which looks really nice but I was wondering whether it is possible to extract selected quality metrics values (i.e., FD mean, number and %) in a file for all the subjects. Some of the dots are really close together and I want to make sure I pick up all the outliers. I can go trough each json file also I guess.
Thank you!
Hi @ElenaP,
MRIQC (version 0.15.0 at least) produces a group_bold.tsv file with columns such as fd_mean', fd_num, and fd_perc, among others, which can be used for your exclusion procedures.
To exclude subjects based on your criteria, you could do the following (in Python):
import pandas as pd
data = pd.read_csv('group_bold.tsv', sep='\t')
select_cols = [col for col in data.columns if 'fd_' in col or 'bids_name' in col]
data = data[select_cols] #Select pertinent columns
data = data[data.fd_perc <= 20] #Exclude subjects if fd_perc > 20%
data.to_csv('group_bold_qc.tsv', sep='\t', index=False)
Where group_bold_qc.tsv is a file containing the subject IDs and FD information for all subjects who pass the exclusion criteria.
Hope I didn’t misinterpret what you were asking.
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