From f20d5ac44bf9e0fdc1723261d1d704cfec9d3af9 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Fri, 23 Aug 2024 12:39:40 -0400 Subject: [PATCH 1/3] Remove unused `--longitudinal` argument (#88) Remove unused `--longitudinal` argument. --- qsirecon/cli/parser.py | 5 ----- qsirecon/config.py | 2 -- tests/get_data.py | 1 - 3 files changed, 8 deletions(-) diff --git a/qsirecon/cli/parser.py b/qsirecon/cli/parser.py index 6d967756..ba40bbe7 100644 --- a/qsirecon/cli/parser.py +++ b/qsirecon/cli/parser.py @@ -245,11 +245,6 @@ def _bids_filter(value, parser): g_conf.add_argument( "--infant", action="store_true", help="configure pipelines to process infant brains" ) - g_conf.add_argument( - "--longitudinal", - action="store_true", - help="Treat dataset as longitudinal - may increase runtime", - ) g_conf.add_argument( "--b0-threshold", "--b0_threshold", diff --git a/qsirecon/config.py b/qsirecon/config.py index 281b72a6..63d9bcb8 100644 --- a/qsirecon/config.py +++ b/qsirecon/config.py @@ -551,8 +551,6 @@ class workflow(_Config): """Any value in the .bval file less than this will be considered a b=0 image.""" infant = False """Configure pipelines specifically for infant brains""" - longitudinal = False - """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag.""" input_type = None """Specifies which pipeline was used to preprocess data in ``bids_dir``.""" recon_spec = None diff --git a/tests/get_data.py b/tests/get_data.py index 8dfab30d..b10c7ec4 100644 --- a/tests/get_data.py +++ b/tests/get_data.py @@ -57,7 +57,6 @@ def get_default_cli_args(): debug=True, low_mem=False, anat_only=False, - longitudinal=False, combine_all_dwis=True, dwi_denoise_window=0, denoise_before_combining=True, From 9b9f8b080ffd48d5db0711ec8a5a6c07f8b65480 Mon Sep 17 00:00:00 2001 From: Philip Cook Date: Fri, 23 Aug 2024 14:54:52 -0400 Subject: [PATCH 2/3] Use file lock to avoid concurrent edits to dataset_description.json (#91) * ENH: use file lock to avoid concurrent edits to dataset_description.json BUG: docker tag in dataset_description was for fmriprep * ENH: Move lock outside the check for file existence Ensures only the first process writes the file * STYLE: fix style issues ENH: Add file lock for the bids ignore file * BUG: docker address is pennlinc not pennbbl --- pyproject.toml | 1 + qsirecon/utils/bids.py | 34 +++++++++++++++++++--------------- 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index dc452272..f594f90d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,7 @@ dependencies = [ 'importlib_resources; python_version < "3.11"', "dipy>=1.8.0,<1.9.0", "dmri-amico == 1.5.4", + "filelock", "fury", "indexed_gzip <= 1.8.7", "jinja2 < 3.1", diff --git a/qsirecon/utils/bids.py b/qsirecon/utils/bids.py index 041a3956..07b9140b 100644 --- a/qsirecon/utils/bids.py +++ b/qsirecon/utils/bids.py @@ -30,6 +30,7 @@ from pathlib import Path from typing import Union +import filelock from bids import BIDSLayout from nipype.pipeline import engine as pe from packaging.version import Version @@ -185,7 +186,7 @@ def write_derivative_description(bids_dir, deriv_dir, dataset_links=None): if "QSIRECON_DOCKER_TAG" in os.environ: dset_desc["GeneratedBy"][0]["Container"] = { "Type": "docker", - "Tag": f"nipreps/fmriprep:{os.environ['QSIRECON_DOCKER_TAG']}", + "Tag": f"pennlinc/qsirecon:{os.environ['QSIRECON_DOCKER_TAG']}", } elif "QSIRECON_SINGULARITY_URL" in os.environ: dset_desc["GeneratedBy"][0]["Container"] = { @@ -215,19 +216,20 @@ def write_derivative_description(bids_dir, deriv_dir, dataset_links=None): dset_desc["DatasetLinks"][key] = str(value) out_dset_description = os.path.join(deriv_dir, "dataset_description.json") - if os.path.isfile(out_dset_description): - with open(out_dset_description, "r") as fo: - old_dset_desc = json.load(fo) - - old_version = old_dset_desc["GeneratedBy"][0]["Version"] - if Version(__version__).public != Version(old_version).public: - config.loggers.utils.warning( - f"Previous output generated by version {old_version} found." - ) - - else: - with open(out_dset_description, "w") as fo: - json.dump(dset_desc, fo, indent=4, sort_keys=True) + lock_file = os.path.join(deriv_dir, "qsirecon_dataset_description.lock") + with filelock.SoftFileLock(lock_file, timeout=60): + if os.path.isfile(out_dset_description): + with open(out_dset_description, "r") as fo: + old_dset_desc = json.load(fo) + + old_version = old_dset_desc["GeneratedBy"][0]["Version"] + if Version(__version__).public != Version(old_version).public: + config.loggers.utils.warning( + f"Previous output generated by version {old_version} found." + ) + else: + with open(out_dset_description, "w") as fo: + json.dump(dset_desc, fo, indent=4, sort_keys=True) def write_bidsignore(deriv_dir): @@ -245,7 +247,9 @@ def write_bidsignore(deriv_dir): ) ignore_file = Path(deriv_dir) / ".bidsignore" - ignore_file.write_text("\n".join(bids_ignore) + "\n") + lock_file = os.path.join(deriv_dir, "qsirecon_bidsignore.lock") + with filelock.SoftFileLock(lock_file, timeout=60): + ignore_file.write_text("\n".join(bids_ignore) + "\n") def validate_input_dir(exec_env, bids_dir, participant_label): From baf517c90e188e36309f5e4a032faa2eeb9c20c9 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Fri, 23 Aug 2024 15:09:09 -0400 Subject: [PATCH 3/3] Make all params and models lower-case (#90) * Make all params lower-case. * Make models lower-case too. * Fix things up. * Fix underscores in entities. * fix * Revert some changes. * Update pyafq_recon_external_trk_outputs.txt --- qsirecon/data/scalars/brainsuite_3dshore.yaml | 36 +++--- qsirecon/data/scalars/dipy_dki.yaml | 18 +-- qsirecon/data/scalars/dipy_mapmri.yaml | 16 +-- qsirecon/data/scalars/dsistudio_gqi.yaml | 10 +- qsirecon/data/scalars/tortoise.yaml | 18 +-- qsirecon/tests/data/amico_noddi_outputs.txt | 2 +- qsirecon/tests/data/autotrack_outputs.txt | 4 +- qsirecon/tests/data/dipy_dki_outputs.txt | 36 +++--- qsirecon/tests/data/dipy_mapmri_outputs.txt | 20 +-- qsirecon/tests/data/mrtrix3_recon_outputs.txt | 14 +-- .../mrtrix_singleshell_ss3t_act_outputs.txt | 14 +-- .../mrtrix_singleshell_ss3t_noact_outputs.txt | 14 +-- ...fq_recon_external_trk_optional_outputs.txt | 2 +- .../data/pyafq_recon_external_trk_outputs.txt | 14 +-- qsirecon/tests/data/scalar_mapper_outputs.txt | 116 +++++++++--------- .../tests/data/tortoise_recon_outputs.txt | 36 +++--- qsirecon/utils/misc.py | 8 ++ qsirecon/workflows/recon/amico.py | 2 +- qsirecon/workflows/recon/dsi_studio.py | 26 ++-- qsirecon/workflows/recon/mrtrix.py | 28 +++-- 20 files changed, 227 insertions(+), 207 deletions(-) diff --git a/qsirecon/data/scalars/brainsuite_3dshore.yaml b/qsirecon/data/scalars/brainsuite_3dshore.yaml index 02ae4e23..d554e448 100644 --- a/qsirecon/data/scalars/brainsuite_3dshore.yaml +++ b/qsirecon/data/scalars/brainsuite_3dshore.yaml @@ -6,44 +6,44 @@ cnr_image: Description: Contrast to noise ratio for 3dSHORE fit lapnorm_file: bids: - model: 3dSHORE + model: 3dshore param: lapnorm metadata: Description: Laplacian norm from regularized MAPMRI (MAPL) mapcoeffs_file: bids: - model: 3dSHORE + model: 3dshore param: mapcoeffs metadata: Description: MAPMRI coefficients msd_file: bids: - model: 3dSHORE - param: MSD + model: 3dshore + param: msd metadata: Description: mean square displacement from MAPMRI ng_file: bids: - model: 3dSHORE - param: NG + model: 3dshore + param: ng metadata: Description: Non-Gaussianity from MAPMRI ngpar_file: bids: - model: 3dSHORE - param: NGpar + model: 3dshore + param: ngpar metadata: Description: Non-Gaussianity parallel from MAPMRI ngperp_file: bids: - model: 3dSHORE - param: NGperp + model: 3dshore + param: ngperp metadata: Description: Non-Gaussianity perpendicular from MAPMRI qiv_file: bids: - model: 3dSHORE - param: QIV + model: 3dshore + param: qiv metadata: Description: q-space inverse variance from MAPMRI r2_image: @@ -54,19 +54,19 @@ regularization_image: Description: regularization of the 3dSHORE fit rtap_file: bids: - model: 3dSHORE - param: RTAP + model: 3dshore + param: rtap metadata: Description: Return to axis probability from MAPMRI rtop_file: bids: - model: 3dSHORE - param: RTOP + model: 3dshore + param: rtop metadata: Description: Return to origin probability from MAPMRI rtpp_file: bids: - model: 3dSHORE - param: RTPP + model: 3dshore + param: rtpp metadata: Description: Return to plane probability from MAPMRI diff --git a/qsirecon/data/scalars/dipy_dki.yaml b/qsirecon/data/scalars/dipy_dki.yaml index 104dd44d..94f201ce 100644 --- a/qsirecon/data/scalars/dipy_dki.yaml +++ b/qsirecon/data/scalars/dipy_dki.yaml @@ -1,54 +1,54 @@ dki_ad: bids: model: dki - param: AD + param: ad metadata: Description: DKI AD dki_ak: bids: model: dki - param: AK + param: ak metadata: Description: DKI AK dki_fa: bids: model: tensor - param: FA + param: fa metadata: Description: DKI FA dki_kfa: bids: model: dki - param: KFA + param: kfa metadata: Description: DKI KFA dki_md: bids: model: dki - param: MD + param: md metadata: Description: DKI MD dki_mk: bids: model: dki - param: MK + param: mk metadata: Description: DKI MK dki_mkt: bids: model: dki - param: MKT + param: mkt metadata: Description: DKI MKT dki_rd: bids: model: dki - param: RD + param: rd metadata: Description: DKI RD dki_rk: bids: model: dki - param: RK + param: rk metadata: Description: DKI RK diff --git a/qsirecon/data/scalars/dipy_mapmri.yaml b/qsirecon/data/scalars/dipy_mapmri.yaml index 76a65dac..a7f3215b 100644 --- a/qsirecon/data/scalars/dipy_mapmri.yaml +++ b/qsirecon/data/scalars/dipy_mapmri.yaml @@ -13,48 +13,48 @@ mapcoeffs_file: msd_file: bids: model: mapmri - param: MSD + param: msd metadata: Description: mean square displacement from MAPMRI ng_file: bids: model: mapmri - param: NG + param: ng metadata: Description: Non-Gaussianity from MAPMRI ngpar_file: bids: model: mapmri - param: NGpar + param: ngpar metadata: Description: Non-Gaussianity parallel from MAPMRI ngperp_file: bids: model: mapmri - param: NGperp + param: ngperp metadata: Description: Non-Gaussianity perpendicular from MAPMRI qiv_file: bids: model: mapmri - param: QIV + param: qiv metadata: Description: q-space inverse variance from MAPMRI rtap_file: bids: model: mapmri - param: RTAP + param: rtap metadata: Description: Return to axis probability from MAPMRI rtop_file: bids: model: mapmri - param: RTOP + param: rtop metadata: Description: Return to origin probability from MAPMRI rtpp_file: bids: model: mapmri - param: RTPP + param: rtpp metadata: Description: Return to plane probability from MAPMRI diff --git a/qsirecon/data/scalars/dsistudio_gqi.yaml b/qsirecon/data/scalars/dsistudio_gqi.yaml index 2de5f731..4a887c7e 100644 --- a/qsirecon/data/scalars/dsistudio_gqi.yaml +++ b/qsirecon/data/scalars/dsistudio_gqi.yaml @@ -12,7 +12,7 @@ dti_fa_file: Description: Radial Diffusivity from a tensor fit gfa_file: bids: - model: GQI + model: gqi param: gfa metadata: Description: Generalized Fractional Anisotropy @@ -24,7 +24,7 @@ ha_file: Description: HA iso_file: bids: - model: GQI + model: gqi param: iso metadata: Description: Isotropic Diffusion @@ -36,19 +36,19 @@ md_file: Description: Mean Diffusivity qa_file: bids: - model: GQI + model: gqi param: qa metadata: Description: Fractional Anisotropy from a tensor fit rd1_file: bids: - model: RDI + model: rdi param: rd1 metadata: Description: RD1 rd2_file: bids: - model: RDI + model: rdi param: rd2 metadata: Description: RD2 diff --git a/qsirecon/data/scalars/tortoise.yaml b/qsirecon/data/scalars/tortoise.yaml index 9acdf5d5..f26aee70 100644 --- a/qsirecon/data/scalars/tortoise.yaml +++ b/qsirecon/data/scalars/tortoise.yaml @@ -7,7 +7,7 @@ ad_file: am_file: bids: model: tensor - param: AM + param: am metadata: Description: A0 from a tensor fit fa_file: @@ -25,31 +25,31 @@ li_file: ng_file: bids: model: mapmri - param: NG + param: ng metadata: Description: Non-Gaussianity from MAPMRI ngpar_file: bids: model: mapmri - param: NGpar + param: ngpar metadata: Description: Non-Gaussianity parallel from MAPMRI ngperp_file: bids: model: mapmri - param: NGperp + param: ngperp metadata: Description: Non-Gaussianity perpendicular from MAPMRI pa_file: bids: model: mapmri - param: PA + param: pa metadata: Description: PA from MAPMRI path_file: bids: model: mapmri - param: PAth + param: path metadata: Description: PAth from MAPMRI rd_file: @@ -61,18 +61,18 @@ rd_file: rtap_file: bids: model: mapmri - param: RTAP + param: rtap metadata: Description: Return to axis probability from MAPMRI rtop_file: bids: model: mapmri - param: RTOP + param: rtop metadata: Description: Return to origin probability from MAPMRI rtpp_file: bids: model: mapmri - param: RTPP + param: rtpp metadata: Description: Return to plane probability from MAPMRI diff --git a/qsirecon/tests/data/amico_noddi_outputs.txt b/qsirecon/tests/data/amico_noddi_outputs.txt index cb6af96b..bd21eae8 100644 --- a/qsirecon/tests/data/amico_noddi_outputs.txt +++ b/qsirecon/tests/data/amico_noddi_outputs.txt @@ -11,7 +11,7 @@ derivatives/qsirecon-NODDI/sub-PNC derivatives/qsirecon-NODDI/sub-PNC.html derivatives/qsirecon-NODDI/sub-PNC/dwi derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwimap.fib.gz -derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-AMICOconfig_dwimap.pickle.gz +derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-amicoconfig_dwimap.pickle.gz derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-direction_dwimap.json derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-direction_dwimap.nii.gz derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-icvf_dwimap.json diff --git a/qsirecon/tests/data/autotrack_outputs.txt b/qsirecon/tests/data/autotrack_outputs.txt index 1a88a134..59cdfb00 100644 --- a/qsirecon/tests/data/autotrack_outputs.txt +++ b/qsirecon/tests/data/autotrack_outputs.txt @@ -10,8 +10,8 @@ derivatives/qsirecon-DSIStudio/logs/CITATION.tex derivatives/qsirecon-DSIStudio/sub-ABCD derivatives/qsirecon-DSIStudio/sub-ABCD.html derivatives/qsirecon-DSIStudio/sub-ABCD/dwi -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-Association_ArcuateFasciculusL_streamlines.tck.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-Association_ArcuateFasciculusR_streamlines.tck.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusL_streamlines.tck.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusR_streamlines.tck.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundlestats.csv derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap.fib.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_mapping.map.gz diff --git a/qsirecon/tests/data/dipy_dki_outputs.txt b/qsirecon/tests/data/dipy_dki_outputs.txt index 3d93198b..3b2a60cc 100644 --- a/qsirecon/tests/data/dipy_dki_outputs.txt +++ b/qsirecon/tests/data/dipy_dki_outputs.txt @@ -10,24 +10,24 @@ derivatives/qsirecon-DKI/logs/CITATION.tex derivatives/qsirecon-DKI/sub-ABCD derivatives/qsirecon-DKI/sub-ABCD.html derivatives/qsirecon-DKI/sub-ABCD/dwi -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AD_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AD_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AK_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AK_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-KFA_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-KFA_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MD_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MD_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MKT_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MKT_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MK_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MK_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RD_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RD_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RK_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RK_dwimap.nii.gz -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-FA_dwimap.json -derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-FA_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ad_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ad_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ak_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ak_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-kfa_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-kfa_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-md_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-md_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mkt_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mkt_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mk_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mk_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rd_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rd_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rk_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rk_dwimap.nii.gz +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.json +derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.nii.gz logs logs/CITATION.bib logs/CITATION.html diff --git a/qsirecon/tests/data/dipy_mapmri_outputs.txt b/qsirecon/tests/data/dipy_mapmri_outputs.txt index f7a88986..489b5390 100644 --- a/qsirecon/tests/data/dipy_mapmri_outputs.txt +++ b/qsirecon/tests/data/dipy_mapmri_outputs.txt @@ -12,16 +12,16 @@ derivatives/qsirecon-DIPYMAPMRI/sub-ABCD.html derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap.fib.gz derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap.mif -derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-MSD_dwimap.json -derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-MSD_dwimap.nii.gz -derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-QIV_dwimap.json -derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-QIV_dwimap.nii.gz -derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-RTAP_dwimap.json -derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-RTAP_dwimap.nii.gz -derivatives/qsirecon-DIPYMAPMRI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-RTOP_dwimap.json 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b/qsirecon/tests/data/mrtrix3_recon_outputs.txt index c300a791..757575f5 100644 --- a/qsirecon/tests/data/mrtrix3_recon_outputs.txt +++ b/qsirecon/tests/data/mrtrix3_recon_outputs.txt @@ -12,13 +12,13 @@ derivatives/qsirecon-MRtrix3_act-FAST/sub-ABCD.html derivatives/qsirecon-MRtrix3_act-FAST/sub-ABCD/dwi derivatives/qsirecon-MRtrix3_act-FAST/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_connectivity.mat derivatives/qsirecon-MRtrix3_act-FAST/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_exemplarbundles.zip -derivatives/qsirecon-MRtrix3_act-FAST/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-SD_Stream_streamlines.tck -derivatives/qsirecon-MRtrix3_act-FAST/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-msmt_csd_param-FOD_label-CSF_dwimap.mif.gz -derivatives/qsirecon-MRtrix3_act-FAST/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-msmt_csd_param-FOD_label-CSF_dwimap.txt 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b/qsirecon/tests/data/mrtrix_singleshell_ss3t_act_outputs.txt index ae693f62..06c26d1b 100644 --- a/qsirecon/tests/data/mrtrix_singleshell_ss3t_act_outputs.txt +++ b/qsirecon/tests/data/mrtrix_singleshell_ss3t_act_outputs.txt @@ -12,17 +12,17 @@ derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC.html derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_connectivity.mat derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_exemplarbundles.zip -derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-SD_Stream_streamlines.tck +derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-sdstream_streamlines.tck derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-mtnorm_param-inliermask_dwimap.nii.gz 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+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-WM_dwimap.txt logs logs/CITATION.bib logs/CITATION.html diff --git a/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt b/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt index abf3c724..11615ce4 100644 --- a/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt +++ b/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt @@ -12,17 +12,17 @@ derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC.html derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC/dwi derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_connectivity.mat derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_exemplarbundles.zip -derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-SD_Stream_streamlines.tck 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+derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-GM_dwimap.txt +derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-WM_dwimap.mif.gz +derivatives/qsirecon-MRtrix3_fork-SS3T_act-None/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-WM_dwimap.txt logs logs/CITATION.bib logs/CITATION.html diff --git a/qsirecon/tests/data/pyafq_recon_external_trk_optional_outputs.txt b/qsirecon/tests/data/pyafq_recon_external_trk_optional_outputs.txt index d31d2b32..a382159f 100644 --- a/qsirecon/tests/data/pyafq_recon_external_trk_optional_outputs.txt +++ b/qsirecon/tests/data/pyafq_recon_external_trk_optional_outputs.txt @@ -2,4 +2,4 @@ derivatives/qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/b derivatives/qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinal_tractography.trk derivatives/qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html derivatives/qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftSuperiorLongitudinalviz_dwi.html -derivatives/qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_space-T1w_dwi_space-RASMM_model-probCSD_algo-AFQ_desc-ARCLviz_dwi.html +derivatives/qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap/viz_core_bundles/sub-ABCD_acq-10per000_space-T1w_dwi_space-RASMM_model-probcsd_algo-AFQ_desc-ARCLviz_dwi.html diff --git a/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt b/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt index 0278d5b6..17b3a2bd 100644 --- a/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt +++ b/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt @@ -10,13 +10,13 @@ derivatives/qsirecon-MRtrix3/logs/CITATION.tex derivatives/qsirecon-MRtrix3/sub-ABCD derivatives/qsirecon-MRtrix3/sub-ABCD.html derivatives/qsirecon-MRtrix3/sub-ABCD/dwi -derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-SD_Stream_streamlines.tck -derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-msmt_csd_param-FOD_label-CSF_dwimap.mif.gz -derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-msmt_csd_param-FOD_label-CSF_dwimap.txt -derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-msmt_csd_param-FOD_label-GM_dwimap.mif.gz 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+derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-msmtcsd_param-fod_label-WM_dwimap.mif.gz +derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-msmtcsd_param-fod_label-WM_dwimap.txt derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mtnorm_param-inliermask_dwimap.nii.gz derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mtnorm_param-norm_dwimap.nii.gz derivatives/qsirecon-MRtrix3/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-sift2_mu.txt diff --git a/qsirecon/tests/data/scalar_mapper_outputs.txt b/qsirecon/tests/data/scalar_mapper_outputs.txt index 1d965733..6c6d8b27 100644 --- a/qsirecon/tests/data/scalar_mapper_outputs.txt +++ b/qsirecon/tests/data/scalar_mapper_outputs.txt @@ -10,43 +10,43 @@ derivatives/qsirecon-DIPYDKI/logs/CITATION.tex derivatives/qsirecon-DIPYDKI/sub-ABCD derivatives/qsirecon-DIPYDKI/sub-ABCD.html derivatives/qsirecon-DIPYDKI/sub-ABCD/dwi 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+derivatives/qsirecon-DIPYDKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rd_dwimap.json +derivatives/qsirecon-DIPYDKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rd_dwimap.nii.gz +derivatives/qsirecon-DIPYDKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rk_dwimap.json +derivatives/qsirecon-DIPYDKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rk_dwimap.nii.gz +derivatives/qsirecon-DIPYDKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.json +derivatives/qsirecon-DIPYDKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.nii.gz derivatives/qsirecon-DSIStudio derivatives/qsirecon-DSIStudio/dataset_description.json derivatives/qsirecon-DSIStudio/logs @@ -57,16 +57,16 @@ derivatives/qsirecon-DSIStudio/logs/CITATION.tex derivatives/qsirecon-DSIStudio/sub-ABCD derivatives/qsirecon-DSIStudio/sub-ABCD.html derivatives/qsirecon-DSIStudio/sub-ABCD/dwi 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derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_model-tensor_param-ad_dwimap.nii.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_model-tensor_param-fa_dwimap.json @@ -89,23 +89,23 @@ derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NL derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_model-tensor_param-tyz_dwimap.nii.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_model-tensor_param-tzz_dwimap.json derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_model-tensor_param-tzz_dwimap.nii.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-Association_ArcuateFasciculusL_streamlines.tck.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-Association_ArcuateFasciculusR_streamlines.tck.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusL_streamlines.tck.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusR_streamlines.tck.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundles-DSIStudio_scalarstats.tsv derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundles-DSIStudio_tdistats.tsv derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundlestats.csv derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap.fib.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_mapping.map.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-GQI_param-gfa_dwimap.json -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-GQI_param-gfa_dwimap.nii.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-GQI_param-iso_dwimap.json -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-GQI_param-iso_dwimap.nii.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-GQI_param-qa_dwimap.json -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-GQI_param-qa_dwimap.nii.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-RDI_param-rd1_dwimap.json -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-RDI_param-rd1_dwimap.nii.gz -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-RDI_param-rd2_dwimap.json -derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-RDI_param-rd2_dwimap.nii.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-gfa_dwimap.json +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-gfa_dwimap.nii.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-iso_dwimap.json +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-iso_dwimap.nii.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-qa_dwimap.json +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-qa_dwimap.nii.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd1_dwimap.json +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd1_dwimap.nii.gz +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd2_dwimap.json +derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd2_dwimap.nii.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ad_dwimap.json derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ad_dwimap.nii.gz derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.json diff --git a/qsirecon/tests/data/tortoise_recon_outputs.txt b/qsirecon/tests/data/tortoise_recon_outputs.txt index 853337ab..10388a2b 100644 --- a/qsirecon/tests/data/tortoise_recon_outputs.txt +++ b/qsirecon/tests/data/tortoise_recon_outputs.txt @@ -10,24 +10,24 @@ derivatives/qsirecon-TORTOISE/logs/CITATION.tex derivatives/qsirecon-TORTOISE/sub-ABCD derivatives/qsirecon-TORTOISE/sub-ABCD.html derivatives/qsirecon-TORTOISE/sub-ABCD/dwi -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-NG_dwimap.json -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-NG_dwimap.nii.gz -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-NGpar_dwimap.json -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-NGpar_dwimap.nii.gz -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-NGperp_dwimap.json -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-NGperp_dwimap.nii.gz -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-PA_dwimap.json -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-PA_dwimap.nii.gz -derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-PAth_dwimap.json 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-derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-AM_dwimap.nii.gz +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-ng_dwimap.json +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-ng_dwimap.nii.gz +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-ngpar_dwimap.json +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-ngpar_dwimap.nii.gz +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-ngperp_dwimap.json +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-ngperp_dwimap.nii.gz +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-pa_dwimap.json 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+derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mapmri_param-rtpp_dwimap.nii.gz +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-am_dwimap.json +derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-am_dwimap.nii.gz derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ad_dwimap.json derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ad_dwimap.nii.gz derivatives/qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.json diff --git a/qsirecon/utils/misc.py b/qsirecon/utils/misc.py index c79cc024..a3c83629 100644 --- a/qsirecon/utils/misc.py +++ b/qsirecon/utils/misc.py @@ -20,3 +20,11 @@ def load_yaml(fname): with open(fname) as f: return yaml.safe_load(f) + + +def remove_non_alphanumeric(input_string: str) -> str: + # Replace all non-alphanumeric characters with an empty string + import re + + cleaned_string = re.sub(r"[^a-zA-Z0-9]", "", input_string) + return cleaned_string diff --git a/qsirecon/workflows/recon/amico.py b/qsirecon/workflows/recon/amico.py index d4c0c0de..d3313e8f 100644 --- a/qsirecon/workflows/recon/amico.py +++ b/qsirecon/workflows/recon/amico.py @@ -162,7 +162,7 @@ def init_amico_noddi_fit_wf( ds_config = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - param="AMICOconfig", + param="amicoconfig", model="noddi", suffix="dwimap", compress=True, diff --git a/qsirecon/workflows/recon/dsi_studio.py b/qsirecon/workflows/recon/dsi_studio.py index 5e3358bc..01847bd9 100644 --- a/qsirecon/workflows/recon/dsi_studio.py +++ b/qsirecon/workflows/recon/dsi_studio.py @@ -37,6 +37,7 @@ from ...interfaces.recon_scalars import DSIStudioReconScalars from ...interfaces.reports import CLIReconPeaksReport, ConnectivityReport from ...utils.bids import clean_datasinks +from ...utils.misc import remove_non_alphanumeric from .utils import init_scalar_output_wf LOGGER = logging.getLogger("nipype.interface") @@ -250,7 +251,7 @@ def init_dsi_studio_tractography_wf( ds_tracking = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model="QAthresh", + model="qathresh", suffix="streamlines", ), name="ds_" + name, @@ -350,6 +351,16 @@ def init_dsi_studio_autotrack_wf( convert_to_tck = pe.MapNode(DSIStudioTrkToTck(), name="convert_to_tck", iterfield="trk_file") + clean_bundle_names = pe.MapNode( + niu.Function( + input_names=["input_string"], + output_names=["bundle"], + function=remove_non_alphanumeric, + ), + name="clean_bundle_names", + iterfield=["input_string"], + ) + # Save tck files of the bundles into the outputs ds_tckfiles = pe.MapNode( DerivativesDataSink( @@ -392,13 +403,12 @@ def init_dsi_studio_autotrack_wf( (actual_trk, ds_mapping, [('map_file', 'in_file')]), (actual_trk, aggregate_atk_results, [ ("native_trk_files", "trk_files"), - ("stat_files", "stat_files")]), - (aggregate_atk_results, convert_to_tck, [ - ("found_bundle_files", "trk_file")]), - (aggregate_atk_results, ds_tckfiles, [ - ("found_bundle_names", "bundle")]), - (convert_to_tck, ds_tckfiles, [ - ("tck_file", "in_file")]), + ("stat_files", "stat_files"), + ]), + (aggregate_atk_results, convert_to_tck, [("found_bundle_files", "trk_file")]), + (aggregate_atk_results, clean_bundle_names, [("found_bundle_names", "input_string")]), + (clean_bundle_names, ds_tckfiles, [("bundle", "bundle")]), + (convert_to_tck, ds_tckfiles, [("tck_file", "in_file")]), (aggregate_atk_results, ds_bundle_csv, [("bundle_csv", "in_file")]), (convert_to_tck, outputnode, [("tck_file", "tck_files")]), (aggregate_atk_results, outputnode, [("found_bundle_names", "bundle_names")]) diff --git a/qsirecon/workflows/recon/mrtrix.py b/qsirecon/workflows/recon/mrtrix.py index 21d1c1c0..488b993a 100644 --- a/qsirecon/workflows/recon/mrtrix.py +++ b/qsirecon/workflows/recon/mrtrix.py @@ -37,6 +37,7 @@ ) from ...interfaces.reports import CLIReconPeaksReport, ConnectivityReport from ...utils.bids import clean_datasinks +from ...utils.misc import remove_non_alphanumeric LOGGER = logging.getLogger("nipype.interface") MULTI_RESPONSE_ALGORITHMS = ("dhollander", "msmt_5tt") @@ -276,11 +277,12 @@ def init_mrtrix_csd_recon_wf( plot_peaks, "mif_file") # fmt:skip if qsirecon_suffix: + model_name = remove_non_alphanumeric(fod_algorithm).lower() ds_wm_odf = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model=fod_algorithm, - param="FOD", + model=model_name, + param="fod", label="WM", suffix="dwimap", extension=".mif.gz", @@ -294,8 +296,8 @@ def init_mrtrix_csd_recon_wf( ds_wm_txt = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model=fod_algorithm, - param="FOD", + model=model_name, + param="fod", label="WM", suffix="dwimap", extension=".txt", @@ -310,8 +312,8 @@ def init_mrtrix_csd_recon_wf( ds_gm_odf = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model=fod_algorithm, - param="FOD", + model=model_name, + param="fod", label="GM", suffix="dwimap", extension=".mif.gz", @@ -325,8 +327,8 @@ def init_mrtrix_csd_recon_wf( ds_gm_txt = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model=fod_algorithm, - param="FOD", + model=model_name, + param="fod", label="GM", suffix="dwimap", extension=".txt", @@ -340,8 +342,8 @@ def init_mrtrix_csd_recon_wf( ds_csf_odf = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model=fod_algorithm, - param="FOD", + model=model_name, + param="fod", label="CSF", suffix="dwimap", extension=".mif.gz", @@ -355,8 +357,8 @@ def init_mrtrix_csd_recon_wf( ds_csf_txt = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model=fod_algorithm, - param="FOD", + model=model_name, + param="fod", label="CSF", suffix="dwimap", extension=".txt", @@ -626,7 +628,7 @@ def init_mrtrix_tractography_wf( ds_tck_file = pe.Node( DerivativesDataSink( dismiss_entities=("desc",), - model=tracking_params["algorithm"], + model=remove_non_alphanumeric(tracking_params["algorithm"]).lower(), suffix="streamlines", extension=".tck", ),