Chris Gorgolewski

Decimate the signal after low-pass filetering

2

Since low-pass filtering changes the effective TR it might be worth decimating (downsampling) the output to save space. This can be performed (in one step together with low-pass filtering) by...

Instead of a set of command line (see #5) switches user should be able to provide one reusable config file specifying: - which regressors to use #10 - highpass cutoff...

Save traces in the output folder: https://reprozip.readthedocs.io/en/1.0.x/packing.html#tracing-an-experiment

[wishlist] Ability to download historical version of precompiled AFNI

3

Right now it is only possible to download current (latest) version of precompiled AFNI. However, to help maintaining packages that depend on AFNI and increase analysis reproducibility it would be...

3dvolreg incorrect exit code and "ERROR: nifti_image_write_hdr_img: NBL does not match nim"

3

3dvolreg exits with code 0 despite errors, produces empty file ``` root@c1af530c4591:/workdir/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-1211283..func..sub-1211283_task-rest_run-05_echo-1_bold.nii.gz/motion_correct# 3dvolreg -Fourier -twopass -1Dfile sub-1211283_task-rest_run-05_echo-1_bold.1D -1Dmatrix_save sub-1211283_task-rest_run-05_echo-1_bold.aff12.1D -prefix sub-1211283_task-rest_run-05_echo-1_bold_volreg.nii.gz -base /workdir/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-1211283..func..sub-1211283_task-rest_run-05_echo-1_bold.nii.gz/gen_ref/ref_image.nii.gz -zpad 4 -maxdisp1D sub-1211283_task-rest_run-05_echo-1_bold_md.1D /workdir/workflow_enumerator/funcMRIQC/_in_file_..data..sub-1211283..func..sub-1211283_task-rest_run-05_echo-1_bold.nii.gz/reorient_and_discard/sub-1211283_task-rest_run-05_echo-1_bold.nii.gz ++ 3dvolreg:...

Add dataset metadata back

2

The metadata was accidentally removed in https://github.com/google-research-datasets/natural-questions/commit/c2c9b2fd85b5b23ae5e313b0d1c2658d1c1cd387.

A Dataset property for denoting how a authors of the dataset should be acknowledge

7

I am looking for a Dataset property that would we a valid place to describe how the authors of a dataset wish to be acknowledged when the data is reused....

Report capable version of the Nipype GIFT Interface. Should be very simple to implement and should be modeled after: https://github.com/poldracklab/niworkflows/blob/7e7a76ced74789932e71298634e2d14fe7c291c3/niworkflows/interfaces/segmentation.py#L103 https://github.com/poldracklab/niworkflows/blob/e486df097e2204e18f42aab1a0fef4d9f33d5608/niworkflows/viz/utils.py#L482 function should be refactored to abstract away code that...

Crop coregistration reports if a mask or a contour is available

1

This will hopefully trim down the size of the reports. Should be easy with this function: http://nilearn.github.io/modules/generated/nilearn.image.crop_img.html

JS based scrolling through volumes

3

Courtesy of @akeshavan http://anisha.pizza/preAFQ/#/report?url=https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fakeshavan-mindcontrol%2Ftests%2FHBN%2FSite-SI%2Fsub-NDARRU600XWW%2Fsess-01%2Fderivatives%2FpreAFQ%2Fpreafq%2Freport%2Freport.json