diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml index c21f96c4..51e25caf 100644 --- a/.github/workflows/python-testing.yml +++ b/.github/workflows/python-testing.yml @@ -148,10 +148,10 @@ jobs: poetry run hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w - name: Test cropseg bids, with path override run: | - poetry run hippunfold - test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz + poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz - name: Test cropseg bids, with path override, left hemi run: | - poetry run hippunfold - test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L + poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L - name: Test T2w with T1w template registration run: | poetry run hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template diff --git a/docs/tutorials/specializedScans.md b/docs/tutorials/specializedScans.md index 3a1f2ad7..7901a8d4 100644 --- a/docs/tutorials/specializedScans.md +++ b/docs/tutorials/specializedScans.md @@ -41,7 +41,7 @@ Here is an example of what the input directory might look like: This can be unfolded with the command: - hippunfold - PATH_TO_OUTPUT_DIR participant --modality cropseg \ + hippunfold . PATH_TO_OUTPUT_DIR participant --modality cropseg \ --path_cropseg exvivo/sub-{subject}/sub-{subject}_hemi-{hemi}_desc-hippo_dseg.nii.gz \ --hemi R --skip_inject_template_labels @@ -87,7 +87,7 @@ hippocampus. Once done, we may have a directory like this: Note that only the last file is needed for unfolding: - hippunfold - PATH_TO_OUTPUT_DIR participant --output_spaces corobl --hemi R --no_reg_template \ + hippunfold . PATH_TO_OUTPUT_DIR participant --output_spaces corobl --hemi R --no_reg_template \ --path_T2w PATH_TO_EXVIVO_DIR/sub-001/sub-001_hemi-R_desc-exvivo_space-CITI168_T2w.nii.gz \ --output_spaces corobl diff --git a/docs/tutorials/standardBIDS.md b/docs/tutorials/standardBIDS.md index f307b104..d8295bb5 100644 --- a/docs/tutorials/standardBIDS.md +++ b/docs/tutorials/standardBIDS.md @@ -79,7 +79,7 @@ HippUnfold will not recognize them without the suffix `_T2w`. We can thus use the `--path_T2w` flag to specify exactly which of these file(s) to use as inputs: - hippunfold - PATH_TO_OUTPUT_DIR participant \ + hippunfold . PATH_TO_OUTPUT_DIR participant \ --path_T1w PATH_TO_nonBIDS_DIR/sub-001_T1w.nii.gz \ --path_T2w PATH_TO_nonBIDS_DIR/sub-{subject}_T2SPACE.nii.gz diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile index a835fc12..0e1d17af 100644 --- a/hippunfold/workflow/Snakefile +++ b/hippunfold/workflow/Snakefile @@ -79,6 +79,7 @@ config.update( participant_label=config["participant_label"], exclude_participant_label=config["exclude_participant_label"], limit_to=list(limit_to_list), + use_bids_inputs=False, ) ) diff --git a/poetry.lock b/poetry.lock index abfdbcee..65daaf04 100644 --- a/poetry.lock +++ b/poetry.lock @@ -879,14 +879,6 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -[[package]] -name = "progress" -version = "1.6" -description = "Easy to use progress bars" -category = "main" -optional = false -python-versions = "*" - [[package]] name = "psutil" version = "5.9.0" @@ -924,16 +916,16 @@ python-versions = ">=2.7, 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