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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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Edge-comp regressors not included in confounds files #2831

Closed sjw42 closed 1 year ago

sjw42 commented 2 years ago

What happened?

I just started preprocessing a data set with fMRIPrep version 22.0.0 and am interested in exploring the newly added edge regressors. However, the edge-comp regressors are not included in the confounds tsv files. I have pasted the headers from one of the confounds files at the bottom of this post. Information about the 24 edge components is included in the corresponding confounds json files and they are listed as retained; e.g. "edge_comp_00": { "CumulativeVarianceExplained": 0.0865755779, "Mask": "Edge", "Method": "EdgeRegressor", "Retained": true, "SingularValue": 404.9880253639, "VarianceExplained": 0.0865755779

------headers from sample confounds file------ global_signal global_signal_derivative1 global_signal_derivative1_power2 global_signal_power2 csf csf_derivative1 csf_derivative1_power2 csf_power2 white_matter white_matter_derivative1 white_matter_derivative1_power2 white_matter_power2 csf_wm tcompcor std_dvars dvars framewise_displacement rmsd t_comp_cor_00 t_comp_cor_01 c_comp_cor_00 c_comp_cor_01 c_comp_cor_02 c_comp_cor_03 c_comp_cor_04 c_comp_cor_05 c_comp_cor_06 w_comp_cor_00 w_comp_cor_01 w_comp_cor_02 w_comp_cor_03 w_comp_cor_04 w_comp_cor_05 w_comp_cor_06 w_comp_cor_07 w_comp_cor_08 w_comp_cor_09 w_comp_cor_10 w_comp_cor_11 w_comp_cor_12 w_comp_cor_13 w_comp_cor_14 w_comp_cor_15 w_comp_cor_16 w_comp_cor_17 w_comp_cor_18 w_comp_cor_19 w_comp_cor_20 w_comp_cor_21 w_comp_cor_22 w_comp_cor_23 w_comp_cor_24 w_comp_cor_25 w_comp_cor_26 w_comp_cor_27 w_comp_cor_28 w_comp_cor_29 w_comp_cor_30 w_comp_cor_31 w_comp_cor_32 w_comp_cor_33 w_comp_cor_34 w_comp_cor_35 w_comp_cor_36 w_comp_cor_37 w_comp_cor_38 w_comp_cor_39 w_comp_cor_40 w_comp_cor_41 w_comp_cor_42 w_comp_cor_43 w_comp_cor_44 w_comp_cor_45 w_comp_cor_46 w_comp_cor_47 w_comp_cor_48 a_comp_cor_00 a_comp_cor_01 a_comp_cor_02 a_comp_cor_03 a_comp_cor_04 a_comp_cor_05 a_comp_cor_06 a_comp_cor_07 a_comp_cor_08 a_comp_cor_09 a_comp_cor_10 a_comp_cor_11 a_comp_cor_12 a_comp_cor_13 a_comp_cor_14 a_comp_cor_15 a_comp_cor_16 a_comp_cor_17 a_comp_cor_18 a_comp_cor_19 a_comp_cor_20 a_comp_cor_21 a_comp_cor_22 a_comp_cor_23 a_comp_cor_24 a_comp_cor_25 a_comp_cor_26 a_comp_cor_27 a_comp_cor_28 a_comp_cor_29 a_comp_cor_30 a_comp_cor_31 a_comp_cor_32 a_comp_cor_33 a_comp_cor_34 a_comp_cor_35 a_comp_cor_36 a_comp_cor_37 a_comp_cor_38 a_comp_cor_39 a_comp_cor_40 a_comp_cor_41 a_comp_cor_42 a_comp_cor_43 a_comp_cor_44 a_comp_cor_45 a_comp_cor_46 a_comp_cor_47 cosine00 cosine01 cosine02 cosine03 non_steady_state_outlier00 non_steady_state_outlier01 non_steady_state_outlier02 non_steady_state_outlier03 trans_x trans_x_derivative1 trans_x_derivative1_power2 trans_x_power2 trans_y trans_y_derivative1 trans_y_derivative1_power2 trans_y_power2 trans_z trans_z_derivative1 trans_z_derivative1_power2 trans_z_power2 rot_x rot_x_derivative1 rot_x_derivative1_power2 rot_x_power2 rot_y rot_y_derivative1 rot_y_derivative1_power2 rot_y_power2 rot_z rot_z_derivative1 rot_z_power2 rot_z_derivative1_power2 motion_outlier00 motion_outlier01 motion_outlier02 motion_outlier03 motion_outlier04 motion_outlier05 motion_outlier06 motion_outlier07 motion_outlier08 motion_outlier09 motion_outlier10 motion_outlier11 motion_outlier12 motion_outlier13 motion_outlier14 motion_outlier15 motion_outlier16 motion_outlier17 motion_outlier18 motion_outlier19 motion_outlier20 motion_outlier21 motion_outlier22 motion_outlier23 motion_outlier24 motion_outlier25 motion_outlier26 motion_outlier27 motion_outlier28 motion_outlier29 motion_outlier30 motion_outlier31 motion_outlier32 motion_outlier33 motion_outlier34 motion_outlier35 motion_outlier36 motion_outlier37 motion_outlier38 motion_outlier39 motion_outlier40 motion_outlier41 motion_outlier42 motion_outlier43 motion_outlier44 motion_outlier45 motion_outlier46 motion_outlier47 motion_outlier48 motion_outlier49 motion_outlier50 motion_outlier51 motion_outlier52 motion_outlier53 motion_outlier54 motion_outlier55 motion_outlier56 motion_outlier57 motion_outlier58 motion_outlier59 motion_outlier60 aroma_motion_01 aroma_motion_02 aroma_motion_03 aroma_motion_04 aroma_motion_05 aroma_motion_06 aroma_motion_08 aroma_motion_09 aroma_motion_10 aroma_motion_11 aroma_motion_12 aroma_motion_16 aroma_motion_21 aroma_motion_25 aroma_motion_27 aroma_motion_28 aroma_motion_29 aroma_motion_30 aroma_motion_31 aroma_motion_33

What command did you use?

singularity run --cleanenv /gpfs/group/sjw42/default/sjw42_collab/sw/singularity/fmriprep/fmriprep_v22.0.0.sif
–participant_label 102
–nthreads 4
–omp-nthreads 3
–low-mem
–skip_bids_validation
–verbose
–longitudinal
–dummy-scans 4
–use-aroma
–output-layout legacy
–output-spaces MNI152NLin6Asym:res-2 MNI152NLin6Asym:res-native
–fs-license-file /gpfs/group/sjw42/default/sjw42_collab/sw/freesurfer-6.0.1/license.txt
–work /gpfs/group/sjw42/default/ASH/DVAL/work
/gpfs/group/sjw42/default/ASH/DVAL/bids
/gpfs/group/sjw42/default/ASH/DVAL/bids/derivatives
participant

What version of fMRIPrep are you running?

22.0.0

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response

burdinskid13 commented 1 year ago

In version 22.0.2 I am still experiencing this issue. Is there a timeline for resolving this? I am very excited to use the edge regressors in my analysis!

effigies commented 1 year ago

Ah, thanks for bumping this. Let me have a quick look and see how difficult this would be to fix...

effigies commented 1 year ago

Okay, I think it's as simple as #2897. Let's let it run and make sure they're in the CI derivatives.