Gal Kepler

Mean Diffusivity turns out low in CSF when reconstructing using ReconstDtiFlow

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## Description **MD** appears to be **low in CSF voxels** when computing it via [DIPY's ReconstDtiFlow](https://dipy.org/documentation/1.5.0/reference/dipy.workflows/#reconstdtiflow) for reconstructing the diffusion tensor. This behavior is somewhat unexpected, especially due to the...

[ENH] Added some options to mrconvert's interface

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## Summary The MRConvert interface now includes some additional available options allowed by the original [MRTrix3's CLI](https://mrtrix.readthedocs.io/en/dev/reference/commands/mrconvert.html). Fixes #3473. ## List of changes proposed in this PR (pull-request) The interface...

### Summary The interface to MRTrix3's mrconvert is missing some useful options (like gradient tables' import & export) ### Actual behavior The basic inputs of mrtrix's interface include out_bvec and...

### Summary I think it'd be helpful to have interfaces for mrtrix3's [transformconvert](https://mrtrix.readthedocs.io/en/latest/reference/commands/transformconvert.html) and [mrtransform](https://mrtrix.readthedocs.io/en/latest/reference/commands/mrtransform.html) functions. I know mrtransform used to have an interface but it seems to be a...

Expanding derivatives' configuration to validate existing BIDS-apps

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Under the assumption that the main goal of this configuration file is to be able to query BIDS-apps' outputs, I think it would be great to validate the correspondence between...

There're some entities missing in both the derivatives' entities configuration and the corresponding default_path_patterns. It would be beneficial to expand this configuration to hold for more BIDS apps' outputs. For...

Keeping track of fMRIPrep.

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This PR includes the following: * Basic workflow's infrastructure now resembles the one initiated in [fmriprep](https://github.com/nipreps/fmriprep/blob/master/fmriprep/workflows/base.py). * [Configurations added to fmriprep](https://fmriprep.org/en/stable/usage.html) are now available in [dmriprep's configuration](https://github.com/GalBenZvi/dmriprep/blob/fmriprep_update/dmriprep/config/config.py) * [Tests' configurations](https://github.com/GalBenZvi/dmriprep/blob/fmriprep_update/dmriprep/data/tests/config.toml)...

I think it's been a while since this repository was initiated to mimic the infrastructure of [fMRIPrep](https://fmriprep.org/en/stable/index.html). Since then, fMRIPrep was updated and upgraded several times. I believe that to...

### Discussed in https://github.com/nipreps/dmriprep/discussions/186 Originally posted by **GalBenZvi** November 22, 2021 Hi all, I've been using **mrtrix3** to process my diffusion data for the past few months and it seems...

Node t1_2_mni failed to run

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Hi, I'm trying to run qsiprep version 0.15.3 and I receive the following error: Node: qsiprep_wf.single_subject_211_wf.anat_preproc_wf.t1_2_mni Working directory: /work/qsiprep_wf/single_subject_211_wf/anat_preproc_wf/t1_2_mni Node inputs: compress_report = auto explicit_masking = True flavor = precise...