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Rename QSIPrep to QSIRecon (#1)
* qsiprep --> qsirecon * pennbbl --> pennlinc * master --> main * Rename folders (qsiprep --> qsirecon) * Address style issues.
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‎.circleci/3TissueAutotrackTest.sh

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -16,8 +16,8 @@ This tests the following features:
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Inputs:
1717
-------
1818
19-
- qsiprep single shell results (data/DSDTI_fmap)
20-
- qsiprep multi shell results (data/DSDTI_fmap)
19+
- qsirecon single shell results (data/DSDTI_fmap)
20+
- qsirecon multi shell results (data/DSDTI_fmap)
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DOC
2323
set +e
@@ -35,10 +35,10 @@ TESTNAME=ss3t_autotrack_test
3535
setup_dir ${TESTDIR}/${TESTNAME}
3636
TEMPDIR=${TESTDIR}/${TESTNAME}/work
3737
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
38-
BIDS_INPUT_DIR=${TESTDIR}/data/singleshell_output/qsiprep
39-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
38+
BIDS_INPUT_DIR=${TESTDIR}/data/singleshell_output/qsirecon
39+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
4040

41-
${QSIPREP_CMD} \
41+
${QSIRECON_CMD} \
4242
-w ${TEMPDIR} \
4343
--recon-input ${BIDS_INPUT_DIR} \
4444
--sloppy \

‎.circleci/3TissueReconTests.sh

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -16,8 +16,8 @@ This tests the following features:
1616
Inputs:
1717
-------
1818
19-
- qsiprep single shell results (data/DSDTI_fmap)
20-
- qsiprep multi shell results (data/DSDTI_fmap)
19+
- qsirecon single shell results (data/DSDTI_fmap)
20+
- qsirecon multi shell results (data/DSDTI_fmap)
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2222
DOC
2323
set +e
@@ -36,10 +36,10 @@ TESTNAME=mrtrix_singleshell_ss3t_test
3636
setup_dir ${TESTDIR}/${TESTNAME}
3737
TEMPDIR=${TESTDIR}/${TESTNAME}/work
3838
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
39-
BIDS_INPUT_DIR=${TESTDIR}/data/singleshell_output/qsiprep
40-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
39+
BIDS_INPUT_DIR=${TESTDIR}/data/singleshell_output/qsirecon
40+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
4141

42-
${QSIPREP_CMD} \
42+
${QSIRECON_CMD} \
4343
-w ${TEMPDIR} \
4444
--recon-input ${BIDS_INPUT_DIR} \
4545
--sloppy \
@@ -53,10 +53,10 @@ TESTNAME=mrtrix_singleshell_ss3t_noACT_test
5353
setup_dir ${TESTDIR}/${TESTNAME}
5454
TEMPDIR=${TESTDIR}/${TESTNAME}/work
5555
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
56-
BIDS_INPUT_DIR=${TESTDIR}/data/singleshell_output/qsiprep
57-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
56+
BIDS_INPUT_DIR=${TESTDIR}/data/singleshell_output/qsirecon
57+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
5858

59-
${QSIPREP_CMD} \
59+
${QSIRECON_CMD} \
6060
-w ${TEMPDIR} \
6161
--recon-input ${BIDS_INPUT_DIR} \
6262
--sloppy \

‎.circleci/AMICOReconTests.sh

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -16,8 +16,8 @@ This tests the following features:
1616
Inputs:
1717
-------
1818
19-
- qsiprep single shell results (data/DSDTI_fmap)
20-
- qsiprep multi shell results (data/DSDTI_fmap)
19+
- qsirecon single shell results (data/DSDTI_fmap)
20+
- qsirecon multi shell results (data/DSDTI_fmap)
2121
2222
DOC
2323
set +e
@@ -36,10 +36,10 @@ TESTNAME=amico_noddi_test
3636
setup_dir ${TESTDIR}/${TESTNAME}
3737
TEMPDIR=${TESTDIR}/${TESTNAME}/work
3838
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
39-
BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsiprep
40-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
39+
BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsirecon
40+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
4141

42-
${QSIPREP_CMD} \
42+
${QSIRECON_CMD} \
4343
-w ${TEMPDIR} \
4444
--recon-input ${BIDS_INPUT_DIR} \
4545
--sloppy \

‎.circleci/AllFieldmaps.sh

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ cat << DOC
55
AllFieldmaps test
66
=================
77
8-
Instead of running full workflows, this test checks that workflows can
8+
Instead of running full workflows, this test checks that workflows can
99
be built for all sorts of fieldmap configurations.
1010
1111
This tests the following features:
@@ -35,9 +35,9 @@ setup_dir ${TESTDIR}/${TESTNAME}
3535
TEMPDIR=${TESTDIR}/${TESTNAME}/work
3636
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
3737
BIDS_INPUT_DIR=${TESTDIR}/data/fmaptests/DSDTI_fmap
38-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
38+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
3939

40-
${QSIPREP_CMD} \
40+
${QSIRECON_CMD} \
4141
-w ${TEMPDIR} \
4242
--boilerplate \
4343
--sloppy --write-graph --mem_mb 4096 \
@@ -49,10 +49,10 @@ setup_dir ${TESTDIR}/${TESTNAME}
4949
TEMPDIR=${TESTDIR}/${TESTNAME}/work
5050
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
5151
BIDS_INPUT_DIR=${TESTDIR}/data/fmaptests/DSCSDSI_fmap
52-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
52+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
5353

5454
# Test blip-up blip-down shelled series (TOPUP/eddy)
55-
${QSIPREP_CMD} \
55+
${QSIRECON_CMD} \
5656
-w ${TEMPDIR} \
5757
--boilerplate \
5858
--hmc-model 3dSHORE \

‎.circleci/AutoTrackTest.sh

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,8 @@ This tests the following features:
1212
Inputs:
1313
-------
1414
15-
- qsiprep single shell results (data/DSDTI_fmap)
16-
- qsiprep multi shell results (data/DSDTI_fmap)
15+
- qsirecon single shell results (data/DSDTI_fmap)
16+
- qsirecon multi shell results (data/DSDTI_fmap)
1717
1818
DOC
1919
set +e
@@ -30,10 +30,10 @@ TESTNAME=autotrack
3030
setup_dir ${TESTDIR}/${TESTNAME}
3131
TEMPDIR=${TESTDIR}/${TESTNAME}/work
3232
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
33-
BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsiprep
34-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
33+
BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsirecon
34+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
3535

36-
${QSIPREP_CMD} \
36+
${QSIRECON_CMD} \
3737
-w ${TEMPDIR} \
3838
--recon-input ${BIDS_INPUT_DIR} \
3939
--sloppy \

‎.circleci/CUDATest.sh

Lines changed: 2 additions & 2 deletions
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@@ -26,10 +26,10 @@ TEMPDIR=${TESTDIR}/${TESTNAME}/work
2626
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
2727
BIDS_INPUT_DIR=${TESTDIR}/data/tinytensor_rpe_series
2828
export FS_LICENSE=${TESTDIR}/data/license.txt
29-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
29+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
3030

3131
# Do the anatomical run on its own
32-
${QSIPREP_CMD} \
32+
${QSIRECON_CMD} \
3333
-w ${TEMPDIR} \
3434
--sloppy \
3535
--anat-modality none \

‎.circleci/DIPYReconTests.sh

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Original file line numberDiff line numberDiff line change
@@ -16,8 +16,8 @@ This tests the following features:
1616
Inputs:
1717
-------
1818
19-
- qsiprep single shell results (data/DSDTI_fmap)
20-
- qsiprep multi shell results (data/DSDTI_fmap)
19+
- qsirecon single shell results (data/DSDTI_fmap)
20+
- qsirecon multi shell results (data/DSDTI_fmap)
2121
2222
DOC
2323
set +e
@@ -36,10 +36,10 @@ TESTNAME=dipy_mapmri_test
3636
setup_dir ${TESTDIR}/${TESTNAME}
3737
TEMPDIR=${TESTDIR}/${TESTNAME}/work
3838
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
39-
BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsiprep
40-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
39+
BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsirecon
40+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
4141

42-
${QSIPREP_CMD} \
42+
${QSIRECON_CMD} \
4343
-w ${TEMPDIR} \
4444
--recon-input ${BIDS_INPUT_DIR} \
4545
--sloppy \
@@ -52,7 +52,7 @@ if [ $? -gt 0 ]; then
5252
fi
5353

5454
# Test dipy DKI
55-
${QSIPREP_CMD} \
55+
${QSIRECON_CMD} \
5656
-w ${TEMPDIR} \
5757
--recon-input ${BIDS_INPUT_DIR} \
5858
--sloppy \

‎.circleci/DRBUDDI_SHORELine_epi.sh

Lines changed: 2 additions & 2 deletions
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@@ -25,10 +25,10 @@ TEMPDIR=${TESTDIR}/${TESTNAME}/work
2525
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
2626
BIDS_INPUT_DIR=${TESTDIR}/data/tinytensor_epi
2727
export FS_LICENSE=${TESTDIR}/data/license.txt
28-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
28+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
2929

3030
# Do the anatomical run on its own
31-
${QSIPREP_CMD} \
31+
${QSIRECON_CMD} \
3232
-w ${TEMPDIR} \
3333
--sloppy \
3434
--anat-modality none \

‎.circleci/DRBUDDI_TENSORLine_epi.sh

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,10 +24,10 @@ TEMPDIR=${TESTDIR}/${TESTNAME}/work
2424
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
2525
BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI
2626
export FS_LICENSE=${TESTDIR}/data/license.txt
27-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
27+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
2828

2929
# Do the anatomical run on its own
30-
${QSIPREP_CMD} \
30+
${QSIRECON_CMD} \
3131
-w ${TEMPDIR} \
3232
--sloppy \
3333
--anat-modality none \

‎.circleci/DRBUDDI_eddy_rpe_series.sh

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,10 +26,10 @@ TEMPDIR=${TESTDIR}/${TESTNAME}/work
2626
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
2727
BIDS_INPUT_DIR=${TESTDIR}/data/tinytensor_rpe_series
2828
export FS_LICENSE=${TESTDIR}/data/license.txt
29-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
29+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
3030

3131
# Do the anatomical run on its own
32-
${QSIPREP_CMD} \
32+
${QSIRECON_CMD} \
3333
-w ${TEMPDIR} \
3434
--sloppy \
3535
--anat-modality none \

‎.circleci/DSCSDSI.sh

Lines changed: 4 additions & 4 deletions
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@@ -7,7 +7,7 @@ DSCSDSI test
77
88
This tests the following features:
99
- Whether the --anat-only workflow is successful
10-
- Whether the regular qsiprep workflow can resume using the
10+
- Whether the regular qsirecon workflow can resume using the
1111
working directory from --anat-only
1212
- The SHORELine motion correction workflow
1313
- Skipping B1 biascorrection
@@ -34,10 +34,10 @@ TEMPDIR=${TESTDIR}/${TESTNAME}/work
3434
OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
3535
BIDS_INPUT_DIR=${TESTDIR}/data/DSCSDSI_nofmap
3636
export FS_LICENSE=${TESTDIR}/data/license.txt
37-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
37+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
3838

39-
# name: Run full qsiprep on DSCSDSI
40-
${QSIPREP_CMD} \
39+
# name: Run full qsirecon on DSCSDSI
40+
${QSIRECON_CMD} \
4141
-w ${TEMPDIR} \
4242
--sloppy --write-graph --use-syn-sdc \
4343
--force-syn \

‎.circleci/DSCSDSI_outputs.txt

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1-
qsiprep
2-
qsiprep/dataset_description.json
3-
qsiprep/dwiqc.json
4-
qsiprep/logs
5-
qsiprep/logs/CITATION.html
6-
qsiprep/logs/CITATION.md
7-
qsiprep/logs/CITATION.tex
8-
qsiprep/sub-tester
9-
qsiprep/sub-tester/anat
10-
qsiprep/sub-tester/anat/sub-tester_desc-brain_mask.nii.gz
11-
qsiprep/sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz
12-
qsiprep/sub-tester/anat/sub-tester_dseg.nii.gz
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qsiprep/sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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qsiprep/sub-tester/anat/sub-tester_from-orig_to-T1w_mode-image_xfm.txt
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qsiprep/sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
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qsiprep/sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz
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qsiprep/sub-tester/anat/sub-tester_label-GM_probseg.nii.gz
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qsiprep/sub-tester/anat/sub-tester_label-WM_probseg.nii.gz
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qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_dseg.nii.gz
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qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
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qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
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qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
25-
qsiprep/sub-tester/dwi
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_dwiqc.json
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-3dSHORE_cnr.nii.gz
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.b
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec
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qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz
36-
qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_dwiref.nii.gz
37-
qsiprep/sub-tester/figures
38-
qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_carpetplot.svg
39-
qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_coreg.svg
40-
qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_desc-resampled_b0ref.svg
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qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_desc-sdc_b0.svg
42-
qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_dwi_denoise_acq_HASC55AP_dwi_wf_denoising.svg
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qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_sampling_scheme.gif
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qsiprep/sub-tester/figures/sub-tester_acq-HASC55AP_shoreline_animation.gif
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qsiprep/sub-tester/figures/sub-tester_seg_brainmask.svg
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qsiprep/sub-tester/figures/sub-tester_t1_2_mni.svg
47-
qsiprep/sub-tester.html
1+
qsirecon
2+
qsirecon/dataset_description.json
3+
qsirecon/dwiqc.json
4+
qsirecon/logs
5+
qsirecon/logs/CITATION.html
6+
qsirecon/logs/CITATION.md
7+
qsirecon/logs/CITATION.tex
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qsirecon/sub-tester
9+
qsirecon/sub-tester/anat
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qsirecon/sub-tester/anat/sub-tester_desc-brain_mask.nii.gz
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qsirecon/sub-tester/anat/sub-tester_desc-preproc_T1w.nii.gz
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qsirecon/sub-tester/anat/sub-tester_dseg.nii.gz
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qsirecon/sub-tester/anat/sub-tester_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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qsirecon/sub-tester/anat/sub-tester_from-orig_to-T1w_mode-image_xfm.txt
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qsirecon/sub-tester/anat/sub-tester_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
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qsirecon/sub-tester/anat/sub-tester_label-CSF_probseg.nii.gz
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qsirecon/sub-tester/anat/sub-tester_label-GM_probseg.nii.gz
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qsirecon/sub-tester/anat/sub-tester_label-WM_probseg.nii.gz
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qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_dseg.nii.gz
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qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
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qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
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qsirecon/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
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qsirecon/sub-tester/dwi
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_confounds.tsv
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-ImageQC_dwi.csv
28+
qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-SliceQC_dwi.json
29+
qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_dwiqc.json
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-3dSHORE_cnr.nii.gz
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-brain_mask.nii.gz
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.b
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bval
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.bvec
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_desc-preproc_dwi.nii.gz
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qsirecon/sub-tester/dwi/sub-tester_acq-HASC55AP_space-T1w_dwiref.nii.gz
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qsirecon/sub-tester/figures
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qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_carpetplot.svg
39+
qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_coreg.svg
40+
qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_desc-resampled_b0ref.svg
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qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_desc-sdc_b0.svg
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qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_dwi_denoise_acq_HASC55AP_dwi_wf_denoising.svg
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qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_sampling_scheme.gif
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qsirecon/sub-tester/figures/sub-tester_acq-HASC55AP_shoreline_animation.gif
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qsirecon/sub-tester/figures/sub-tester_seg_brainmask.svg
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qsirecon/sub-tester/figures/sub-tester_t1_2_mni.svg
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qsirecon/sub-tester.html
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/tmp/DSCSDSI/derivatives

‎.circleci/DSDTI_TOPUP.sh

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -33,10 +33,10 @@ TEMPDIR=${TESTDIR}/${TESTNAME}/work
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OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
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BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI
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export FS_LICENSE=${TESTDIR}/data/license.txt
36-
QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
36+
QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
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# Do the anatomical run on its own
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${QSIPREP_CMD} \
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${QSIRECON_CMD} \
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-w ${TEMPDIR} \
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--sloppy \
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--unringing-method mrdegibbs \

‎.circleci/DSDTI_nofmap.sh

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -32,13 +32,13 @@ TEMPDIR=${TESTDIR}/${TESTNAME}/work
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OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
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BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI
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export FS_LICENSE=${TESTDIR}/data/license.txt
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QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
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QSIRECON_CMD=$(run_qsirecon_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
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# CRITICAL: delete the fieldmap data
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rm -rf data/DSDTI/sub-PNC/fmap
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# Do the anatomical run on its own
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${QSIPREP_CMD} \
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${QSIRECON_CMD} \
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-w ${TEMPDIR} \
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--eddy-config ${EDDY_CFG} \
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--denoise-method none \

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