From ef0d11da5ecea1a56ac9a08a08ee27fa63f8d0d5 Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Tue, 13 Aug 2024 14:02:19 -0400 Subject: [PATCH] update expected outputs --- .circleci/AllFieldmaps.sh | 64 ---------- .circleci/DRBUDDI_SHORELine_epi.sh | 43 ------- .circleci/DRBUDDI_TENSORLine_epi.sh | 40 ------ .circleci/DRBUDDI_eddy_rpe_series.sh | 43 ------- .circleci/DSCSDSI.sh | 51 -------- .circleci/DSCSDSI_outputs.txt | 48 ------- .circleci/DSDTI_TOPUP.sh | 49 -------- .circleci/DSDTI_nofmap.sh | 49 -------- .circleci/DSDTI_nofmap_outputs.txt | 48 ------- .circleci/DSDTI_outputs.txt | 117 ------------------ .circleci/DSDTI_synfmap.sh | 53 -------- .circleci/DSDTI_synsdc_outputs.txt | 48 ------- .circleci/HBCD_preproc.sh | 44 ------- .circleci/IntramodalTemplate.sh | 49 -------- .circleci/IntramodalTemplate_outputs.txt | 69 ----------- .circleci/MultiT1w.sh | 87 ------------- .circleci/get_data.sh | 4 +- .circleci/testing_eddy_params.json | 0 qsirecon/tests/data/amico_noddi_outputs.txt | 2 +- qsirecon/tests/data/autotrack_outputs.txt | 2 +- qsirecon/tests/data/dipy_dki_outputs.txt | 2 +- qsirecon/tests/data/dipy_mapmri_outputs.txt | 2 +- qsirecon/tests/data/mrtrix3_recon_outputs.txt | 2 +- .../mrtrix_singleshell_ss3t_act_outputs.txt | 2 +- .../mrtrix_singleshell_ss3t_noact_outputs.txt | 2 +- .../data/pyafq_recon_external_trk_outputs.txt | 2 +- .../tests/data/pyafq_recon_full_outputs.txt | 2 +- qsirecon/tests/data/scalar_mapper_outputs.txt | 2 +- .../tests/data/tortoise_recon_outputs.txt | 2 +- 29 files changed, 13 insertions(+), 915 deletions(-) delete mode 100644 .circleci/AllFieldmaps.sh delete mode 100644 .circleci/DRBUDDI_SHORELine_epi.sh delete mode 100644 .circleci/DRBUDDI_TENSORLine_epi.sh delete mode 100644 .circleci/DRBUDDI_eddy_rpe_series.sh delete mode 100644 .circleci/DSCSDSI.sh delete mode 100644 .circleci/DSCSDSI_outputs.txt delete mode 100644 .circleci/DSDTI_TOPUP.sh delete mode 100644 .circleci/DSDTI_nofmap.sh delete mode 100644 .circleci/DSDTI_nofmap_outputs.txt delete mode 100644 .circleci/DSDTI_outputs.txt delete mode 100644 .circleci/DSDTI_synfmap.sh delete mode 100644 .circleci/DSDTI_synsdc_outputs.txt delete mode 100644 .circleci/HBCD_preproc.sh delete mode 100644 .circleci/IntramodalTemplate.sh delete mode 100644 .circleci/IntramodalTemplate_outputs.txt delete mode 100644 .circleci/MultiT1w.sh delete mode 100644 .circleci/testing_eddy_params.json diff --git a/.circleci/AllFieldmaps.sh b/.circleci/AllFieldmaps.sh deleted file mode 100644 index 3ba6c289..00000000 --- a/.circleci/AllFieldmaps.sh +++ /dev/null @@ -1,64 +0,0 @@ -#!/bin/bash - -cat << DOC - -AllFieldmaps test -================= - -Instead of running full workflows, this test checks that workflows can -be built for all sorts of fieldmap configurations. - -This tests the following features: - - Blip-up + Blip-down DWI series for TOPUP/Eddy - - Eddy is run on a CPU - - Denoising is skipped - - A follow-up reconstruction using the dsi_studio_gqi workflow - -Inputs: -------- - - - DSDTI BIDS data (data/DSDTI_fmap) - -DOC -set +e -source ./get_data.sh -TESTDIR=${PWD} -get_config_data ${TESTDIR} -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json -export FS_LICENSE=${TESTDIR}/data/license.txt -get_bids_data ${TESTDIR} fmaps - -# Test blip-up blip-down shelled series (TOPUP/eddy) -TESTNAME=DTI_SDC -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/fmaptests/DSDTI_fmap -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --boilerplate \ - --sloppy --write-graph --mem_mb 4096 \ - -vv --output-resolution 5 - -# Test blip-up blip-down non-shelled series (SHORELine/sdcflows) -TESTNAME=DSI_SDC -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/fmaptests/DSCSDSI_fmap -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# Test blip-up blip-down shelled series (TOPUP/eddy) -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --boilerplate \ - --hmc-model 3dSHORE \ - --sloppy --write-graph --mem_mb 4096 \ - -vv --output-resolution 5 - - - - diff --git a/.circleci/DRBUDDI_SHORELine_epi.sh b/.circleci/DRBUDDI_SHORELine_epi.sh deleted file mode 100644 index 5f96db3a..00000000 --- a/.circleci/DRBUDDI_SHORELine_epi.sh +++ /dev/null @@ -1,43 +0,0 @@ -#!/bin/bash - -cat << DOC - -Test EPI fieldmap correction with SHORELine + DRBUDDI -===================================================== - -This tests the following features: - - SHORELine (here, just b=0 registration) motion correction - - - -DOC - -set +e -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=DRBUDDI_SHORELINE_EPI -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} drbuddi_epi -CFG=${TESTDIR}/data/nipype.cfg - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/tinytensor_epi -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# Do the anatomical run on its own -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --sloppy \ - --anat-modality none \ - --denoise-method none \ - --b1-biascorrect-stage none \ - --pepolar-method DRBUDDI \ - --hmc-model none \ - --output-resolution 2 \ - --shoreline-iters 1 \ - -vv --stop-on-first-crash - - diff --git a/.circleci/DRBUDDI_TENSORLine_epi.sh b/.circleci/DRBUDDI_TENSORLine_epi.sh deleted file mode 100644 index 7d6fd48c..00000000 --- a/.circleci/DRBUDDI_TENSORLine_epi.sh +++ /dev/null @@ -1,40 +0,0 @@ -#!/bin/bash - -cat << DOC - -Test EPI fieldmap correction with TENSORLine + DRBUDDI -====================================================== - -This tests the following features: - - TENSORLine (tensor-based) motion correction - -DOC - -set +e -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=DRBUDDI_TENSORLINE_EPI -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} DSDTI -CFG=${TESTDIR}/data/nipype.cfg - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# Do the anatomical run on its own -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --sloppy \ - --anat-modality none \ - --denoise-method none \ - --b1-biascorrect-stage none \ - --pepolar-method DRBUDDI \ - --hmc-model tensor \ - --output-resolution 2 \ - --shoreline-iters 1 \ - -vv --stop-on-first-crash \ No newline at end of file diff --git a/.circleci/DRBUDDI_eddy_rpe_series.sh b/.circleci/DRBUDDI_eddy_rpe_series.sh deleted file mode 100644 index 7583bd6f..00000000 --- a/.circleci/DRBUDDI_eddy_rpe_series.sh +++ /dev/null @@ -1,43 +0,0 @@ -#!/bin/bash - -cat << DOC - -Test paired DWI series with DRBUDDI -=================================== - -This tests the following features: - - Eddy is run on a CPU - - DRBUDDI is run with two DWI series - -DOC - -set +e -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=DRBUDDI_RPE -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} drbuddi_rpe_series -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/tinytensor_rpe_series -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# Do the anatomical run on its own -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --sloppy \ - --anat-modality none \ - --denoise-method none \ - --b1_biascorrect_stage none \ - --pepolar-method DRBUDDI \ - --eddy_config ${EDDY_CFG} \ - --output-resolution 5 \ - -vv --stop-on-first-crash - - diff --git a/.circleci/DSCSDSI.sh b/.circleci/DSCSDSI.sh deleted file mode 100644 index 7c192888..00000000 --- a/.circleci/DSCSDSI.sh +++ /dev/null @@ -1,51 +0,0 @@ -#!/bin/bash - -cat << DOC - -DSCSDSI test -============ - -This tests the following features: - - Whether the --anat-only workflow is successful - - Whether the regular qsirecon workflow can resume using the - working directory from --anat-only - - The SHORELine motion correction workflow - - Skipping B1 biascorrection - - Using the SyN-SDC distortion correction method - -Inputs: -------- - - - DSCSDSI BIDS data (data/DSCSDSI_nofmap) - -DOC -set +e -# Setup environment and get data -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=DSCSDSI -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} DSCSDSI -CFG=${TESTDIR}/data/nipype.cfg - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/DSCSDSI_nofmap -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# name: Run full qsirecon on DSCSDSI -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --sloppy --write-graph --use-syn-sdc \ - --force-syn \ - --b1_biascorrect_stage none \ - --hmc_model 3dSHORE \ - --hmc-transform Rigid \ - --shoreline_iters 1 \ - --output-resolution 5 \ - --stop-on-first-crash \ - -vv - diff --git a/.circleci/DSCSDSI_outputs.txt b/.circleci/DSCSDSI_outputs.txt deleted file mode 100644 index dbc0cfca..00000000 --- a/.circleci/DSCSDSI_outputs.txt +++ /dev/null @@ -1,48 +0,0 @@ -qsirecon -qsirecon/dataset_description.json -qsirecon/dwiqc.json -qsirecon/logs -qsirecon/logs/CITATION.html -qsirecon/logs/CITATION.md -qsirecon/logs/CITATION.tex -qsirecon/sub-tester -qsirecon/sub-tester/anat -qsirecon/sub-tester/anat/sub-tester_desc-brain_mask.nii.gz -qsirecon/sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz -qsirecon/sub-tester/anat/sub-tester_dseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -qsirecon/sub-tester/anat/sub-tester_from-orig_to-T1w_mode-image_xfm.txt -qsirecon/sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsirecon/sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_label-GM_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_label-WM_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_dseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz -qsirecon/sub-tester/dwi -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_dwiqc.json -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-3dSHORE_cnr.nii.gz -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.b -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz -qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_dwiref.nii.gz -qsirecon/sub-tester/figures -qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_carpetplot.svg -qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_coreg.svg -qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_desc-resampled_b0ref.svg -qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_desc-sdc_b0.svg -qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_dwi_denoise_acq_HASC55AP_dwi_wf_denoising.svg -qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_sampling_scheme.gif -qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_shoreline_animation.gif -qsirecon/sub-tester/figures/sub-tester_seg_brainmask.svg -qsirecon/sub-tester/figures/sub-tester_t1_2_mni.svg -qsirecon/sub-tester.html -/tmp/DSCSDSI/derivatives diff --git a/.circleci/DSDTI_TOPUP.sh b/.circleci/DSDTI_TOPUP.sh deleted file mode 100644 index 9fb4beb4..00000000 --- a/.circleci/DSDTI_TOPUP.sh +++ /dev/null @@ -1,49 +0,0 @@ -#!/bin/bash - -cat << DOC - -DSCDTI_TOPUP test -================= - -This tests the following features: - - TOPUP on a single-shell sequence - - Eddy is run on a CPU - - mrdegibbs is run - - A follow-up reconstruction using the dsi_studio_gqi workflow - -Inputs: -------- - - - DSDTI BIDS data (data/DSDTI) - -DOC - -set +e -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=DSDTI_TOPUP -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} DSDTI -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# Do the anatomical run on its own -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --sloppy \ - --unringing-method mrdegibbs \ - --b1-biascorrect-stage legacy \ - --recon-spec dsi_studio_gqi \ - --eddy_config ${EDDY_CFG} \ - --output-resolution 5 \ - -vv - - diff --git a/.circleci/DSDTI_nofmap.sh b/.circleci/DSDTI_nofmap.sh deleted file mode 100644 index a334ed0b..00000000 --- a/.circleci/DSDTI_nofmap.sh +++ /dev/null @@ -1,49 +0,0 @@ -#!/bin/bash - -cat << DOC - -DSCDTI_nofmap test -================== - -This tests the following features: - - A workflow with no distortion correction followed by eddy - - Eddy is run on a CPU - - Denoising is skipped - - A follow-up reconstruction using the dsi_studio_gqi workflow - -Inputs: -------- - - - DSDTI BIDS data (data/DSDTI) - -DOC -set +e -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=DSDTI_nofmap -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} DSDTI -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# CRITICAL: delete the fieldmap data -rm -rf data/DSDTI/sub-PNC/fmap - -# Do the anatomical run on its own -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --eddy-config ${EDDY_CFG} \ - --denoise-method none \ - --unringing-method rpg \ - --b1-biascorrect-stage none \ - --sloppy \ - --output-resolution 5 \ - -vv diff --git a/.circleci/DSDTI_nofmap_outputs.txt b/.circleci/DSDTI_nofmap_outputs.txt deleted file mode 100644 index ed902888..00000000 --- a/.circleci/DSDTI_nofmap_outputs.txt +++ /dev/null @@ -1,48 +0,0 @@ -qsirecon -qsirecon/dataset_description.json -qsirecon/dwiqc.json -qsirecon/logs -qsirecon/logs/CITATION.html -qsirecon/logs/CITATION.md -qsirecon/logs/CITATION.tex -qsirecon/sub-PNC -qsirecon/sub-PNC/anat -qsirecon/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_dseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -qsirecon/sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt -qsirecon/sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsirecon/sub-PNC/anat/sub-PNC_label-CSF_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_label-GM_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_label-WM_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_dseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz -qsirecon/sub-PNC/dwi -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz -qsirecon/sub-PNC/figures -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_carpetplot.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_coreg.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_desc-resampled_b0ref.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_desc-sdc_b0.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_dwi_denoise_acq_realistic_dwi_wf_biascorr.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_dwi_denoise_acq_realistic_dwi_wf_denoising.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_sampling_scheme.gif -qsirecon/sub-PNC/figures/sub-PNC_seg_brainmask.svg -qsirecon/sub-PNC/figures/sub-PNC_t1_2_mni.svg -qsirecon/sub-PNC.html -/tmp/DSDTI/nofmap_derivatives diff --git a/.circleci/DSDTI_outputs.txt b/.circleci/DSDTI_outputs.txt deleted file mode 100644 index cfec9cc2..00000000 --- a/.circleci/DSDTI_outputs.txt +++ /dev/null @@ -1,117 +0,0 @@ -qsirecon -qsirecon/dataset_description.json -qsirecon/dwiqc.json -qsirecon/logs -qsirecon/logs/CITATION.html -qsirecon/logs/CITATION.md -qsirecon/logs/CITATION.tex -qsirecon/sub-PNC -qsirecon/sub-PNC/anat -qsirecon/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_dseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -qsirecon/sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt -qsirecon/sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsirecon/sub-PNC/anat/sub-PNC_label-CSF_probseg.nii.gz 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index f1fc48aa..00000000 --- a/.circleci/DSDTI_synfmap.sh +++ /dev/null @@ -1,53 +0,0 @@ -#!/bin/bash - -cat << DOC - -DSCDTI_nofmap test -================== - -This tests the following features: - - A workflow with no distortion correction followed by eddy - - Eddy is run on a CPU - - Denoising is skipped - - A follow-up reconstruction using the dsi_studio_gqi workflow - -Inputs: -------- - - - DSDTI BIDS data (data/DSDTI) - -DOC -set +e - -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=DSDTI_nofmap -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} DSDTI -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# CRITICAL: delete the fieldmap data -rm -rf data/DSDTI/sub-PNC/fmap - - -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --eddy-config ${EDDY_CFG} \ - --sloppy \ - --force-syn \ - --b1-biascorrect-stage final \ - --denoise-method none \ - --output-resolution 5 \ - -vv - - - diff --git a/.circleci/DSDTI_synsdc_outputs.txt b/.circleci/DSDTI_synsdc_outputs.txt deleted file mode 100644 index a94a9fac..00000000 --- a/.circleci/DSDTI_synsdc_outputs.txt +++ /dev/null @@ -1,48 +0,0 @@ -qsirecon -qsirecon/dataset_description.json -qsirecon/dwiqc.json -qsirecon/logs -qsirecon/logs/CITATION.html -qsirecon/logs/CITATION.md -qsirecon/logs/CITATION.tex -qsirecon/sub-PNC -qsirecon/sub-PNC/anat -qsirecon/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_dseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -qsirecon/sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt -qsirecon/sub-PNC/anat/sub-PNC_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsirecon/sub-PNC/anat/sub-PNC_label-CSF_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_label-GM_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_label-WM_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_dseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz -qsirecon/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz -qsirecon/sub-PNC/dwi -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_confounds.tsv -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_desc-ImageQC_dwi.csv -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_desc-SliceQC_dwi.json -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-brain_mask.nii.gz -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-eddy_cnr.nii.gz -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.b -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bval -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.bvec -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_dwi.nii.gz -qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwiref.nii.gz -qsirecon/sub-PNC/figures -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_carpetplot.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_coreg.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_desc-resampled_b0ref.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_desc-sdc_b0.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_dwi_denoise_acq_realistic_dwi_wf_biascorr.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_dwi_denoise_acq_realistic_dwi_wf_denoising.svg -qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_sampling_scheme.gif -qsirecon/sub-PNC/figures/sub-PNC_seg_brainmask.svg -qsirecon/sub-PNC/figures/sub-PNC_t1_2_mni.svg -qsirecon/sub-PNC.html -/tmp/DSDTI/synfmap_derivatives diff --git a/.circleci/HBCD_preproc.sh b/.circleci/HBCD_preproc.sh deleted file mode 100644 index 6767ecde..00000000 --- a/.circleci/HBCD_preproc.sh +++ /dev/null @@ -1,44 +0,0 @@ -#!/bin/bash - -cat << DOC - -Test paired DWI series with DRBUDDI -=================================== - -This tests the following features: - - Eddy is run on a CPU - - DRBUDDI is run with two DWI series - -DOC - -set +e -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=HBCD -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} HBCD -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/hbcd_sim -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# Do the HBCD-style run -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --sloppy \ - --anat-modality T2w \ - --infant \ - --denoise-method dwidenoise \ - --b1_biascorrect_stage none \ - --pepolar-method DRBUDDI \ - --eddy_config ${EDDY_CFG} \ - --output-resolution 5 \ - -vv --stop-on-first-crash - - diff --git a/.circleci/IntramodalTemplate.sh b/.circleci/IntramodalTemplate.sh deleted file mode 100644 index 42afef6d..00000000 --- a/.circleci/IntramodalTemplate.sh +++ /dev/null @@ -1,49 +0,0 @@ -#!/bin/bash - -cat << DOC - -IntramodalTemplate test -======================= - -A two-session dataset is used to create an intramodal template. - -This tests the following features: - - Blip-up + Blip-down DWI series for TOPUP/Eddy - - Eddy is run on a CPU - - Denoising is skipped - - A follow-up reconstruction using the dsi_studio_gqi workflow - -Inputs: -------- - - - twoses BIDS data (data/DSDTI_fmap) - -DOC -set +e - -source ./get_data.sh -TESTDIR=${PWD} -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} twoses -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json -export FS_LICENSE=${TESTDIR}/data/license.txt - -# Test blip-up blip-down shelled series (TOPUP/eddy) -TESTNAME=imtemplate -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/twoses -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --sloppy \ - --b1_biascorrect_stage none \ - --hmc_model none \ - --b0-motion-corr-to first \ - --output-resolution 5 \ - --intramodal-template-transform BSplineSyN \ - --intramodal-template-iters 2 \ - -vv diff --git a/.circleci/IntramodalTemplate_outputs.txt b/.circleci/IntramodalTemplate_outputs.txt deleted file mode 100644 index a7519928..00000000 --- a/.circleci/IntramodalTemplate_outputs.txt +++ /dev/null @@ -1,69 +0,0 @@ -qsirecon -qsirecon/dataset_description.json -qsirecon/dwiqc.json -qsirecon/logs -qsirecon/logs/CITATION.html -qsirecon/logs/CITATION.md -qsirecon/logs/CITATION.tex -qsirecon/sub-tester -qsirecon/sub-tester/anat -qsirecon/sub-tester/anat/sub-tester_desc-brain_mask.nii.gz -qsirecon/sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz -qsirecon/sub-tester/anat/sub-tester_dseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 -qsirecon/sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 -qsirecon/sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_label-GM_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_label-WM_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_dseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz -qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz -qsirecon/sub-tester/figures -qsirecon/sub-tester/figures/sub-tester_imtcoreg.svg -qsirecon/sub-tester/figures/sub-tester_seg_brainmask.svg -qsirecon/sub-tester/figures/sub-tester_ses-1_acq-HASC55PA_carpetplot.svg -qsirecon/sub-tester/figures/sub-tester_ses-1_acq-HASC55PA_coreg.svg -qsirecon/sub-tester/figures/sub-tester_ses-1_acq-HASC55PA_desc-resampled_b0ref.svg -qsirecon/sub-tester/figures/sub-tester_ses-1_acq-HASC55PA_dwi_denoise_ses_1_acq_HASC55PA_dwi_wf_biascorr.svg -qsirecon/sub-tester/figures/sub-tester_ses-1_acq-HASC55PA_sampling_scheme.gif -qsirecon/sub-tester/figures/sub-tester_ses-1_acq-HASC55PA_tointramodal.svg -qsirecon/sub-tester/figures/sub-tester_ses-2_acq-HASC55AP_carpetplot.svg -qsirecon/sub-tester/figures/sub-tester_ses-2_acq-HASC55AP_coreg.svg -qsirecon/sub-tester/figures/sub-tester_ses-2_acq-HASC55AP_desc-resampled_b0ref.svg -qsirecon/sub-tester/figures/sub-tester_ses-2_acq-HASC55AP_dwi_denoise_ses_2_acq_HASC55AP_dwi_wf_biascorr.svg -qsirecon/sub-tester/figures/sub-tester_ses-2_acq-HASC55AP_sampling_scheme.gif -qsirecon/sub-tester/figures/sub-tester_ses-2_acq-HASC55AP_tointramodal.svg -qsirecon/sub-tester/figures/sub-tester_t1_2_mni.svg -qsirecon/sub-tester.html -qsirecon/sub-tester/ses-1 -qsirecon/sub-tester/ses-1/anat -qsirecon/sub-tester/ses-1/anat/sub-tester_ses-1_from-orig_to-T1w_mode-image_xfm.txt -qsirecon/sub-tester/ses-1/dwi -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_confounds.tsv -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-ImageQC_dwi.csv -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-SliceQC_dwi.json -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_dwiqc.json -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-brain_mask.nii.gz -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-none_cnr.nii.gz -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.b -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.bval -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.bvec -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_desc-preproc_dwi.nii.gz -qsirecon/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-T1w_dwiref.nii.gz -qsirecon/sub-tester/ses-2 -qsirecon/sub-tester/ses-2/dwi -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_confounds.tsv -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-ImageQC_dwi.csv -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-SliceQC_dwi.json -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_dwiqc.json -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-none_cnr.nii.gz -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.b -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz -qsirecon/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-T1w_dwiref.nii.gz -/tmp/twoses/derivatives diff --git a/.circleci/MultiT1w.sh b/.circleci/MultiT1w.sh deleted file mode 100644 index ac0566b9..00000000 --- a/.circleci/MultiT1w.sh +++ /dev/null @@ -1,87 +0,0 @@ -#!/bin/bash - -cat << DOC - -MultiT1w test -================== - -This tests the following features: - - freesurfer's robust template - -Inputs: -------- - - - DSDTI BIDS data (data/DSDTI) - -DOC -set +e - -source ./get_data.sh -TESTDIR=${PWD} -TESTNAME=MultiT1w -get_config_data ${TESTDIR} -get_bids_data ${TESTDIR} DSDTI -CFG=${TESTDIR}/data/nipype.cfg -EDDY_CFG=${TESTDIR}/data/eddy_config.json - -# For the run -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives -BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI -export FS_LICENSE=${TESTDIR}/data/license.txt -QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR}) - -# CRITICAL: delete the fieldmap data -rm -rf data/DSDTI/sub-PNC/fmap - -# Create a shifted version of the t1w -if [[ "${IN_CI}" = 'true' ]]; then - 3dWarp \ - -matvec_in2out 'MATRIX(1,0,0,2,0,1,0,4,0,0,1,1)' \ - -gridset ${BIDS_INPUT_DIR}/sub-PNC/anat/sub-PNC_T1w.nii.gz \ - -prefix ${BIDS_INPUT_DIR}/sub-PNC/anat/sub-PNC_run-02_T1w.nii.gz \ - ${BIDS_INPUT_DIR}/sub-PNC/anat/sub-PNC_T1w.nii.gz -else - docker run -u $(id -u) \ - -v ${BIDS_INPUT_DIR}:/BIDS \ - --rm -ti --entrypoint 3dWarp \ - ${IMAGE} \ - -matvec_in2out 'MATRIX(1,0,0,2,0,1,0,4,0,0,1,1)' \ - -gridset /BIDS/sub-PNC/anat/sub-PNC_T1w.nii.gz \ - -prefix /BIDS/sub-PNC/anat/sub-PNC_run-02_T1w.nii.gz \ - /BIDS/sub-PNC/anat/sub-PNC_T1w.nii.gz - -fi - -cp ${BIDS_INPUT_DIR}/sub-PNC/anat/sub-PNC_T1w.json \ - ${BIDS_INPUT_DIR}/sub-PNC/anat/sub-PNC_run-02_T1w.json - -# Do the anatomical run on its own -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --eddy-config ${EDDY_CFG} \ - --denoise-method none \ - --sloppy \ - --output-resolution 5 \ - --anat-only \ - -vv - - -# Explicitly test --longitudinal -TESTNAME=Longitudinal -setup_dir ${TESTDIR}/${TESTNAME} -TEMPDIR=${TESTDIR}/${TESTNAME}/work -OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives - -${QSIRECON_CMD} \ - -w ${TEMPDIR} \ - --eddy-config ${EDDY_CFG} \ - --denoise-method none \ - --sloppy \ - --output-resolution 5 \ - --anat-only \ - --longitudinal \ - -vv - - diff --git a/.circleci/get_data.sh b/.circleci/get_data.sh index 7c648b1c..938beb13 100644 --- a/.circleci/get_data.sh +++ b/.circleci/get_data.sh @@ -309,8 +309,8 @@ Contents: ^^^^^^^^^ - data/singleshell_output/qsirecon/dataset_description.json - - data/singleshell_output/qsirecon/logs/CITATION.html - - data/singleshell_output/qsirecon/logs/CITATION.md + - data/singleshell_output/logs/CITATION.html + - data/singleshell_output/logs/CITATION.md - data/singleshell_output/qsirecon/logs/CITATION.tex - data/singleshell_output/qsirecon/sub-PNC/anat/sub-PNC_desc-brain_mask.nii.gz - data/singleshell_output/qsirecon/sub-PNC/anat/sub-PNC_desc-preproc_T1w.nii.gz diff --git a/.circleci/testing_eddy_params.json b/.circleci/testing_eddy_params.json deleted file mode 100644 index e69de29b..00000000 diff --git a/qsirecon/tests/data/amico_noddi_outputs.txt b/qsirecon/tests/data/amico_noddi_outputs.txt index 45f9fd25..46628b9c 100644 --- a/qsirecon/tests/data/amico_noddi_outputs.txt +++ b/qsirecon/tests/data/amico_noddi_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/autotrack_outputs.txt b/qsirecon/tests/data/autotrack_outputs.txt index 1ca20d7a..43e1f2dc 100644 --- a/qsirecon/tests/data/autotrack_outputs.txt +++ b/qsirecon/tests/data/autotrack_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/dipy_dki_outputs.txt b/qsirecon/tests/data/dipy_dki_outputs.txt index edfbea31..a5f1b6ba 100644 --- a/qsirecon/tests/data/dipy_dki_outputs.txt +++ b/qsirecon/tests/data/dipy_dki_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/dipy_mapmri_outputs.txt b/qsirecon/tests/data/dipy_mapmri_outputs.txt index ce43e9d3..191ac054 100644 --- a/qsirecon/tests/data/dipy_mapmri_outputs.txt +++ b/qsirecon/tests/data/dipy_mapmri_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/mrtrix3_recon_outputs.txt b/qsirecon/tests/data/mrtrix3_recon_outputs.txt index 8ff1ae21..a301bb7a 100644 --- a/qsirecon/tests/data/mrtrix3_recon_outputs.txt +++ b/qsirecon/tests/data/mrtrix3_recon_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/mrtrix_singleshell_ss3t_act_outputs.txt b/qsirecon/tests/data/mrtrix_singleshell_ss3t_act_outputs.txt index 9b58803b..ce34034a 100644 --- a/qsirecon/tests/data/mrtrix_singleshell_ss3t_act_outputs.txt +++ b/qsirecon/tests/data/mrtrix_singleshell_ss3t_act_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt b/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt index ba6e4d1e..763784db 100644 --- a/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt +++ b/qsirecon/tests/data/mrtrix_singleshell_ss3t_noact_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt b/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt index 424b1614..74d57ded 100644 --- a/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt +++ b/qsirecon/tests/data/pyafq_recon_external_trk_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/pyafq_recon_full_outputs.txt b/qsirecon/tests/data/pyafq_recon_full_outputs.txt index 00b666e2..af33133c 100644 --- a/qsirecon/tests/data/pyafq_recon_full_outputs.txt +++ b/qsirecon/tests/data/pyafq_recon_full_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/scalar_mapper_outputs.txt b/qsirecon/tests/data/scalar_mapper_outputs.txt index a80b4a2e..f823663b 100644 --- a/qsirecon/tests/data/scalar_mapper_outputs.txt +++ b/qsirecon/tests/data/scalar_mapper_outputs.txt @@ -1,5 +1,5 @@ qsirecon -qsirecon/dataset_description.json +dataset_description.json qsirecon/dwiqc.json logs logs/CITATION.bib diff --git a/qsirecon/tests/data/tortoise_recon_outputs.txt b/qsirecon/tests/data/tortoise_recon_outputs.txt index e8cd0fcd..ee7ea8a0 100644 --- a/qsirecon/tests/data/tortoise_recon_outputs.txt +++ b/qsirecon/tests/data/tortoise_recon_outputs.txt @@ -2,7 +2,7 @@ qsirecon dataset_description.json qsirecon/dwiqc.json logs -CITATION.bib +logs/CITATION.bib logs/CITATION.html logs/CITATION.md logs/CITATION.tex