PR1119 Review #1
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…eprocessing utils (aramis-lab#1116) * Move DWI specific functions from filemanip utils to dwi utils preproc pipeline utils * Fix typing that works only for Python >= 3.10 * Clean api
Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.2.0 to 10.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@10.2.0...10.3.0) --- updated-dependencies: - dependency-name: pillow dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* add definition for FWHM * add link for FWHM
* add definition for SUVR in glossary and link in ML_prepareSVM description * Update docs/glossary.md --------- Co-authored-by: Gensollen <[email protected]>
…ramis-lab#1127) * Check that BIDS folders have a dataset_description.json file * make the _check_bids_is_not_empty function a bit more robust
* Use an enum for the study names * update unit tests * forgot one
Bumps [idna](https://github.com/kjd/idna) from 3.6 to 3.7. - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](kjd/idna@v3.6...v3.7) --- updated-dependencies: - dependency-name: idna dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* refactor freesurfer pipelines * add forgotten cli * use absolute imports in task definitions * allow string or Path for get_subject_id * fix folder creation in init_input_node
* run linter on maint branches * run unit tests on maint branches * run converter non regression tests on maint branches * run instantiation tests on maint branches
* run linter on maint branches * run unit tests on maint branches * run converter non regression tests on maint branches * run instantiation tests on maint branches
…lab#1153) * move bids version definition * update unit tests
* update OASIS website URL * Apply suggestions from code review
aramis-lab#1159) * Wrong Processed sequence --> Results: Impossible to make bids of FDG PET Uniform (does not find it) * Linter exception * Linter word-list exception update * Update clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fdg_pet.py Co-authored-by: Gensollen <[email protected]> * Update pyproject.toml Co-authored-by: Gensollen <[email protected]> * Update clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fdg_pet.py Co-authored-by: Gensollen <[email protected]> * Update clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fdg_pet.py * try using a text file for ignoring words * remove useless codespell:ignore * sort ignore words --------- Co-authored-by: Gensollen <[email protected]>
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Hello @tharpm95, I have a small question regarding the function 'rename_maps' since I am not yet totally familiar with fmaps and corresponding dcm2nix outputs. Could you tell me what you are expecting at the output of dcm2nix in terms of files (json/nifti) and what you want to do with them ? |
Sure. First of all, thank-you for the PR, it has run successfully without issues. I will go ahead and merge the request unless you want to add more? Regarding the fmaps, there is a PDF which I have referenced which provides file naming convention information. I tried to follow BIDS specification version 1.1.1 section 8.3.5.1 Case 1 and Case 2. The file names listed in that specification are what is expected as outputs from dcm2niix. The reason that we want the fmaps is because we are processing resting state fMRI data for all ADNI participants at our center, and we would like to convert the data to BIDS before processing. However, without also having the field maps, we cannot correct for magnetic field distortions thus limiting our analyses. I hope that this answers your question. |
Thanks for your answer, that's clearer ! I will be working on the PR you opened on Clinica after this so you can close my PR. |
With this PR :
The modifications allowing the code to run properly are inside clinica/iotools/converters/adni_to_bids/adni_utils.py :
create_adni_sessions_dictwas removedmod_to_updateinside the functioncreate_filewas also removedDo not hesitate if you have questions or comments.