Julien Sein

First experience with v21.0.0: SDC with topup worse than 3dQwarp?

1

### What happened? Thank you again for the tremendous work around fmriprep and NiPreps in general! Curious about the topup implementation for SDC, I compared the output for the same...

[mcflirt related behaviour] Wrong motion parameters estimates in confounds_timeseries.tsv (lot of zeros!)

16

### What version of fMRIPrep are you using? FMRIPREP v 20.2.1 ### What kind of installation are you using? Containers (Singularity, Docker), or "bare-metal"? Singularity installation (version 2.6.1-dist), running on...

issue with mcflirt using SBref as reference when subject doesn't move

11

Hi, I am not exactely a HCPPipelines user but rather a FMRIPREP user but I noticed an issue with a methodology that I was derived from the one used by...

Bug in QSIPREP reconstruction pipeline when using --dwi-only

4

Originally posted on [Neurostars](https://neurostars.org/t/help-with-qsiprep-reconstruction-pipeline-command/22811), I was directed to QSIPREP GitHub to see if there is a bug or if I did a mistake on the command line: I am trying...

Error with eddy_cuda with option -repol

2

I encounter this error message when running qsiprep v0.14.3 on a singularity container ``` EDDY::: DoVolumeToVolumeRegistration: Unable to find volume with no outliers in shell 0 with b-value=300 ``` The...

issue when using "method":"lsr" with eddy

2

Hi I am using qsiprep v0.14.3 with singularity on HCP with cuda capabilities. I wanted to use eddy_cuda with `--resamp=lsr` within qsiprep an I did so using the `eddy_params.json` file...

error with eddy (open_mp or cuda)

4

This an issue for a dataset for which we acquired the same set set of directions in AP and PA. QSIPREP worked fine for the full data set. For the...

Options when subjects fail in crop_aladin stage

1

Inspired from subject `sub-032159` in `site-mountsinai-S` from PRIME-DE, which fail miserably since the first step of macapype. Here is for instance the image after the first stage: - **option 1**...

Version flag doesn't work and need to Update --deid options

1

Thank you for this great tool! I use it for my research and it works well! Here is message on a tiny buy to help improving the documentation about the...

Coregistration failing randomly between tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz and SBref

1

### What happened? I noticed that for one of the run (out of 6 with identical acquisition settings) of the subject we test with fmriprep v23.2.0a2, the image sub-SUB_task-TASK_run-RUN_space-T1w_boldref.nii.gz was...