pni-lab PUMI issues - Githubissues

pni-lab / PUMI

PUMI: neuroimaging Pipelines Using Modular workflow Integration

https://pumi.readthedocs.io/en/latest/

GNU General Public License v3.0

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Use create_dataset_description instead of save_software_versions in the HCP pipelines

#191 khoffschlag opened 1 month ago
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Make datalad datasets usable as input datasets for cluster script

#190 khoffschlag opened 1 month ago
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Decrease slurm job deadline to 3 hours

#189 khoffschlag closed 1 month ago
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Fix problem with timeseries qc images (memory leaking)

#188 khoffschlag closed 4 months ago
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Improve cluster script & HCP pipeline

#187 khoffschlag closed 4 months ago
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Create dataset_description.json for derivatives

#186 khoffschlag closed 4 months ago
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Make 'software_versions.txt' more BIDS-compliant

#185 khoffschlag closed 4 months ago
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Fix critical bugs and integrate new features

#184 khoffschlag closed 7 months ago
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After the merge of "slurmify-pumi" branch, create new git tag

#183 khoffschlag opened 7 months ago
1
Missing scripts in pyproject.toml

#182 khoffschlag closed 7 months ago
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versioneer is not able to fetch PUMI version

#181 khoffschlag closed 7 months ago
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Bug in add_argument statement for bbr (bbr will always be False)

#180 khoffschlag closed 7 months ago
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Check if the results of the fieldmap_correction workflow are correct

#179 khoffschlag opened 7 months ago
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Sink used PUMI version in derivatives

#178 khoffschlag closed 7 months ago
1
Deepbet requirement missing in requirements.txt

#177 khoffschlag closed 7 months ago
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Adapt PUMI for newer python versions

#176 khoffschlag closed 7 months ago
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deepbet does not work in pumi docker container anymore

#175 khoffschlag closed 7 months ago
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Add apptainer script and HCP pipeline

#174 khoffschlag closed 8 months ago
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Fix func2standard

#173 khoffschlag closed 8 months ago
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Dockerfile_v0.6 - GLIBCXX_3.4.30 not found

#172 khoffschlag closed 7 months ago
1
Create minified container based on Dockerfile_v0.6

#171 khoffschlag opened 10 months ago
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Can not build Dockerfile

#170 khoffschlag closed 7 months ago
2
Integrate "deepbet" brain extraction tool

#169 khoffschlag closed 7 months ago
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Support brain extraction of functional images with HD-Bet

#168 khoffschlag opened 10 months ago
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Delete problem-causing file

#167 khoffschlag closed 7 months ago
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Update "Start developing PUMI on Windows" docs

#166 khoffschlag opened 10 months ago
1
use func2standard

#165 khoffschlag closed 8 months ago
1
fix rcpl pipeline for docker use

#164 khoffschlag closed 11 months ago
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Integrate RCPL model

#163 khoffschlag closed 11 months ago
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Sink unscrubbed FD

#162 khoffschlag closed 1 year ago
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integrate func2standard & fix bet qc images generation

#161 khoffschlag closed 1 year ago
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fix regex for GroupsPipeline

#160 khoffschlag closed 1 year ago
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Fix func2anat qc generation

#159 khoffschlag closed 1 year ago
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suffix specified when getting t1w images with BidsPipeline

#158 spisakt closed 1 year ago
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138 structural diffusion weighted imaging mrtrix3

#157 mhmadAbs opened 1 year ago
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BidsApp does not work with --help

#156 khoffschlag closed 7 months ago
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add tutorial on how to run PUMI pipeline in our docker container

#155 khoffschlag closed 1 year ago
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Merge test_atlas

#154 khoffschlag closed 1 year ago
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add MRtrix3 to Dockerfile

#153 khoffschlag closed 1 year ago
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get_ref_locally has no fallback value for 'ventricle_mask'

#152 khoffschlag opened 1 year ago
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update requirements.txt

#151 khoffschlag closed 1 year ago
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Create new Dockerfile that uses scikit-learn version 1.1.2

#150 khoffschlag closed 1 year ago
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Problems with the atlas_selection pipeline in combination with the MultiProc plugin

#149 khoffschlag closed 1 year ago
0
"Permission denied" when running some pipelines with run_pumi_docker

#148 khoffschlag closed 1 year ago
1
rpn_signature_timeseries_.py creates unwanted folders in the derivatives folder

#147 khoffschlag closed 1 year ago
1
fix issue #145

#146 khoffschlag closed 1 year ago
0
check if the output_dir and working_dir parameters are tackled well in the new BidsApp implementaqtion

#145 spisakt closed 1 year ago
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add runtime arguments to CLI - close #142

#144 khoffschlag closed 1 year ago
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compatibility fixes for FSL 6.0.1

#143 khoffschlag closed 1 year ago
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run_args cli parameter

#142 khoffschlag closed 1 year ago
0