ajschadler12

Handling ABCD GE pepolar sequences and other split-files.

4

**Is your feature request related to a problem? Please describe.** When dcm2niix converts an ABCD-style GE pepolar sequence (i.e. blip-up and blip-down as single spin-echo series), it normally splits it...

[FEATURE REQUEST] Saving Eddy-outputs in output folder for use in EddyQC

9

In order to use FSL's EddyQC with data preprocessed using qsiprep, I need to save the working directory locally using `-w WORK_DIR`. Is there an option to save the necessary...

Docker_CPU downloads weights to /root/.tractseg, creating complications when running as singularity container

3

For the purposes of running TractSeg on a local compute cluster, I converted the docker container to a singularity image. However, since `Docker_CPU` downloads the pre-trained weights to `/root/.tractseg/`, the...

# Preamble pybids version: `bids.__version__ --> '0.15.2'` Issue is referenced with example code in [this neurostars thread](https://neurostars.org/t/bids-bidslayout-build-path-removes-dir-label-from-dwi-images/23485). Issue is confirmed to not affect `bold` or `epi` files. # Issue ##...

* **What is the current behavior?** * Run `-proc_dwi` without `-autotract` and without `-keep_tck`. (Exit successfully) * Rerun `-proc_dwi` with `-autotract`. * AutoTract exits due to lack of `tck` tractogram...

fschfiletype from fsl v6.0.0 destroys data when working with float32 or uint16 T1w images. Upgrading to v6.0.5 fixes issue.

1

* **What is the current behavior?** * fschfiletype program from fsl v6.0.0 (default in micapipe docker image) destroys T1w data when working with uint16 or float32 T1-weighted images. * **Please...

Independent DWI sequences are concatenated in final output when processed together.

1

* **What is the current behavior?** 1. Include two different DWI sequences. (single and multi-shell) 2. Include two EPI images for distortion correction of respective DWI sequences. 3. The two...

[Question] Acqparams in case of multiple b0s

5

My apologies for the basic question: In the case of multiple concatenated b0 images, should the acqparams.txt contain _n+1_ rows, _n_ being the number of b0 volumes?