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Set output directory for derivative datasinks #914

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merged 6 commits into from
Jan 14, 2025
Merged

Set output directory for derivative datasinks #914

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f449d99
Fix datasinks?
tsalo Jan 13, 2025
f6523fd
Change topupcsv filename.
tsalo Jan 14, 2025
4afdce2
Update tortoise.py
tsalo Jan 14, 2025
e117fc4
Merge branch 'master' into fix-ds
tsalo Jan 14, 2025
a866b9d
Update filenames in .circleci too.
tsalo Jan 14, 2025
bd5d5b0
Update preprocessing.rst
tsalo Jan 14, 2025
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2 changes: 1 addition & 1 deletion .circleci/DSCSDSI_outputs.txt
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Expand Up @@ -23,7 +23,7 @@ qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-GM_probseg.ni
qsiprep/sub-tester/anat/sub-tester_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
qsiprep/sub-tester/dwi
qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_desc-confounds_timeseries.tsv
qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-image_qc.csv
qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-image_qc.tsv
qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-slice_qc.json
qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_dwiqc.json
qsiprep/sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_model-3dSHORE_stat-cnr_dwimap.json
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2 changes: 1 addition & 1 deletion .circleci/DSDTI_nofmap_outputs.txt
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Expand Up @@ -23,7 +23,7 @@ qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
qsiprep/sub-PNC/dwi
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-confounds_timeseries.tsv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.csv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.tsv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-slice_qc.json
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz
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2 changes: 1 addition & 1 deletion .circleci/DSDTI_outputs.txt
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Expand Up @@ -23,7 +23,7 @@ qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
qsiprep/sub-PNC/dwi
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-confounds_timeseries.tsv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.csv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.tsv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-slice_qc.json
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz
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2 changes: 1 addition & 1 deletion .circleci/DSDTI_synsdc_outputs.txt
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Expand Up @@ -23,7 +23,7 @@ qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
qsiprep/sub-PNC/anat/sub-PNC_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
qsiprep/sub-PNC/dwi
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_desc-confounds_timeseries.tsv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.csv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.tsv
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-slice_qc.json
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_dwiqc.json
qsiprep/sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz
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4 changes: 2 additions & 2 deletions .circleci/IntramodalTemplate_outputs.txt
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Expand Up @@ -42,7 +42,7 @@ qsiprep/sub-tester/ses-1/anat
qsiprep/sub-tester/ses-1/anat/sub-tester_ses-1_from-orig_to-T1w_mode-image_xfm.txt
qsiprep/sub-tester/ses-1/dwi
qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_desc-confounds_timeseries.tsv
qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-image_qc.csv
qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-image_qc.tsv
qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-slice_qc.json
qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_dwiqc.json
qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_desc-brain_mask.nii.gz
Expand All @@ -56,7 +56,7 @@ qsiprep/sub-tester/ses-1/dwi/sub-tester_ses-1_acq-HASC55PA_space-ACPC_dwiref.nii
qsiprep/sub-tester/ses-2
qsiprep/sub-tester/ses-2/dwi
qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_desc-confounds_timeseries.tsv
qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-image_qc.csv
qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-image_qc.tsv
qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-slice_qc.json
qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_dwiqc.json
qsiprep/sub-tester/ses-2/dwi/sub-tester_ses-2_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz
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2 changes: 1 addition & 1 deletion docs/preprocessing.rst
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Expand Up @@ -384,7 +384,7 @@ working on specific gradient strengths or directions.
Quality Control Data
====================

A single-line csv file (``desc-image_qc.csv``) is created for each output
A single-line tsv file (``desc-image_qc.tsv``) is created for each output
image. This file is particularly useful for comparing the relative quality
across subjects before deciding who to include in a group analysis. The
columns in this file come from DSI Studio's QC calculation and is described
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2 changes: 1 addition & 1 deletion qsiprep/data/io_spec.json
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Expand Up @@ -27,7 +27,7 @@
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<dwiref>|dwiref}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<dwi>|dwi}.{extension<nii|nii.gz|b|b_table.txt|bval|bvec|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<timeseries|dwi|topupcsv|hmcOptimization|qc>|timeseries}.{extension<tsv|csv|json>|tsv}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<timeseries|dwi|hmcOptimization|qc>|timeseries}.{extension<tsv|csv|json>|tsv}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<bvecs>|bvecs}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_model-{model}][_stat-{statistic}][_desc-{desc}]_{suffix<dwimap>|dwimap}.{extension<nii|nii.gz|json>|nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<fmapreg|fmapregvsm|b0ref>|fmapreg}.{extension<nii|nii.gz|json>|nii.gz}",
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6 changes: 3 additions & 3 deletions qsiprep/interfaces/eddy.py
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Expand Up @@ -57,7 +57,7 @@ class GatherEddyInputsOutputSpec(TraitedSpec):
pre_topup_image = File(exists=True)
eddy_acqp = File(exists=True)
eddy_first = File(exists=True)
b0_csv = File(exists=True)
b0_tsv = File(exists=True)
eddy_indices = File(exists=True)
forward_transforms = traits.List()
forward_warps = traits.List()
Expand Down Expand Up @@ -86,7 +86,7 @@ class GatherEddyInputs(SimpleInterface):
def _run_interface(self, runtime):
# Gather inputs for TOPUP
topup_prefix = op.join(runtime.cwd, 'topup_')
topup_datain_file, topup_imain_file, topup_text, b0_csv, topup0, eddy0 = (
topup_datain_file, topup_imain_file, topup_text, b0_tsv, topup0, eddy0 = (
get_best_b0_topup_inputs_from(
dwi_file=self.inputs.dwi_file,
bval_file=self.inputs.bval_file,
Expand All @@ -102,7 +102,7 @@ def _run_interface(self, runtime):
self._results['topup_datain'] = topup_datain_file
self._results['topup_imain'] = topup_imain_file
self._results['topup_report'] = topup_text
self._results['b0_csv'] = b0_csv
self._results['b0_tsv'] = b0_tsv
self._results['topup_first'] = topup0
self._results['eddy_first'] = eddy0

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12 changes: 6 additions & 6 deletions qsiprep/interfaces/epi_fmap.py
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Expand Up @@ -270,22 +270,22 @@ def get_best_b0_topup_inputs_from(
by=['same_as_first', 'index'], ascending=[False, True], inplace=True
)

imain_output = cwd + '/topup_imain.nii.gz'
imain_output = op.join(cwd, 'topup_imain.nii.gz')
imain_img = concat_imgs(
[to_lps(img, new_axcodes=('L', 'A', 'S')) for img in sdc_selections['nii_3d_files']],
auto_resample=True,
)
imain_img.to_filename(imain_output)

datain_file = cwd + '/topup_datain.txt'
datain_file = op.join(cwd, 'topup_datain.txt')
with open(datain_file, 'w') as f:
f.write('\n'.join(sdc_selections['fsl_spec']))

b0_csv = cwd + '/b0_selection_info.csv'
dwi_b0_df.drop('nii_3d_files', 1).to_csv(b0_csv, index=False)
b0_tsv = op.join(cwd, 'b0_selection_info.tsv')
dwi_b0_df.drop('nii_3d_files', 1).to_csv(b0_tsv, sep='\t', index=False)

# get out reference images from the topup and eddy data
topup_reg_file = cwd + '/topup_reg_image.nii.gz'
topup_reg_file = op.join(cwd, 'topup_reg_image.nii.gz')
index_img(imain_output, 0).to_filename(topup_reg_file)

topup_report = topup_selection_to_report(
Expand All @@ -298,7 +298,7 @@ def get_best_b0_topup_inputs_from(
datain_file,
imain_output,
topup_report,
b0_csv,
b0_tsv,
topup_reg_file,
dwi_b0_df.loc[0, 'nii_3d_files'],
)
Expand Down
4 changes: 2 additions & 2 deletions qsiprep/interfaces/reports.py
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Expand Up @@ -554,8 +554,8 @@ def _run_interface(self, runtime):
image_qc['file_name'] = output_file
bids_info = get_bids_params(output_file)
image_qc.update(bids_info)
output = op.join(runtime.cwd, 'dwi_qc.csv')
pd.DataFrame(image_qc).to_csv(output, index=False)
output = op.join(runtime.cwd, 'dwi_qc.tsv')
pd.DataFrame(image_qc).to_csv(output, sep='\t', index=False)
self._results['series_qc_file'] = output
return runtime

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4 changes: 2 additions & 2 deletions qsiprep/interfaces/tortoise.py
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Expand Up @@ -150,7 +150,7 @@ def _run_interface(self, runtime):
elif self.inputs.fieldmap_type == 'epi':
# Use the same function that was used to get images for TOPUP, but get the images
# directly from the CSV
_, _, _, b0_csv, _, _ = get_best_b0_topup_inputs_from(
_, _, _, b0_tsv, _, _ = get_best_b0_topup_inputs_from(
dwi_file=self.inputs.dwi_files,
bval_file=bval_files,
b0_threshold=self.inputs.b0_threshold,
Expand All @@ -161,7 +161,7 @@ def _run_interface(self, runtime):
raw_image_sdc=self.inputs.raw_image_sdc,
)

b0s_df = pd.read_csv(b0_csv)
b0s_df = pd.read_table(b0_tsv)
selected_images = b0s_df[b0s_df.selected_for_sdc].reset_index(drop=True)
up_row = selected_images.loc[0]
down_row = selected_images.loc[1]
Expand Down
6 changes: 3 additions & 3 deletions qsiprep/tests/data/drbuddi_rpe_outputs.txt
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Expand Up @@ -9,9 +9,7 @@ sub-tinytensors.html
sub-tinytensors/dwi
sub-tinytensors/dwi/sub-tinytensors_desc-confounds_timeseries.tsv
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-brain_mask.nii.gz
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-image_qc.csv
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-image_qc.tsv
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.b_table.txt
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.bval
Expand All @@ -20,3 +18,5 @@ sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.json
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-preproc_dwi.nii.gz
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_desc-slice_qc.json
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_dwiref.nii.gz
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-tinytensors/dwi/sub-tinytensors_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
6 changes: 3 additions & 3 deletions qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt
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Expand Up @@ -9,9 +9,7 @@ sub-tinytensors.html
sub-tinytensors/dwi
sub-tinytensors/dwi/sub-tinytensors_dir-PA_desc-confounds_timeseries.tsv
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-brain_mask.nii.gz
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-image_qc.csv
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_model-none_stat-cnr_dwimap.json
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_model-none_stat-cnr_dwimap.nii.gz
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-image_qc.tsv
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.b_table.txt
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.bval
Expand All @@ -20,3 +18,5 @@ sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.json
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-preproc_dwi.nii.gz
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_desc-slice_qc.json
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_dwiref.nii.gz
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_model-none_stat-cnr_dwimap.json
sub-tinytensors/dwi/sub-tinytensors_dir-PA_space-ACPC_model-none_stat-cnr_dwimap.nii.gz
4 changes: 2 additions & 2 deletions qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt
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Expand Up @@ -9,14 +9,14 @@ sub-PNC.html
sub-PNC/dwi
sub-PNC/dwi/sub-PNC_acq-realistic_desc-confounds_timeseries.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.csv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bvec
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-slice_qc.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-tensor_stat-cnr_dwimap.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-tensor_stat-cnr_dwimap.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz
6 changes: 3 additions & 3 deletions qsiprep/tests/data/dscsdsi_outputs.txt
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Expand Up @@ -19,10 +19,8 @@ sub-tester/anat/sub-tester_space-ACPC_desc-preproc_T1w.nii.gz
sub-tester/anat/sub-tester_space-ACPC_dseg.nii.gz
sub-tester/dwi
sub-tester/dwi/sub-tester_acq-HASC55AP_desc-confounds_timeseries.tsv
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_model-3dSHORE_stat-cnr_dwimap.json
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_model-3dSHORE_stat-cnr_dwimap.nii.gz
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-brain_mask.nii.gz
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-image_qc.csv
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-image_qc.tsv
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.b_table.txt
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.bval
Expand All @@ -31,3 +29,5 @@ sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.json
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-preproc_dwi.nii.gz
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_desc-slice_qc.json
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_dwiref.nii.gz
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_model-3dSHORE_stat-cnr_dwimap.json
sub-tester/dwi/sub-tester_acq-HASC55AP_space-ACPC_model-3dSHORE_stat-cnr_dwimap.nii.gz
7 changes: 4 additions & 3 deletions qsiprep/tests/data/dsdti_nofmap_outputs.txt
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Expand Up @@ -19,10 +19,9 @@ sub-PNC/anat/sub-PNC_space-ACPC_desc-preproc_T1w.nii.gz
sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz
sub-PNC/dwi
sub-PNC/dwi/sub-PNC_acq-realistic_desc-confounds_timeseries.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_desc-pepolar_qc.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.csv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval
Expand All @@ -31,3 +30,5 @@ sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-slice_qc.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
6 changes: 3 additions & 3 deletions qsiprep/tests/data/dsdti_synfmap_outputs.txt
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Expand Up @@ -20,9 +20,7 @@ sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz
sub-PNC/dwi
sub-PNC/dwi/sub-PNC_acq-realistic_desc-confounds_timeseries.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.csv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval
Expand All @@ -31,3 +29,5 @@ sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-slice_qc.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
6 changes: 3 additions & 3 deletions qsiprep/tests/data/dsdti_topup_outputs.txt
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is the pepolar_qc supposed to appear in this one?

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It looks like dsdti_topup is defined in the pytest markers but there's no corresponding test in the tests/ folder.

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Also, is it weird that dsdti_nofmap is creating this file?

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I think in the previous setup, DSDTI_nofmap downloaded data that had fieldmaps, then deleted those fieldmaps in a script. So this new nofmap is actually running with a pepolar fieldmap

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We should probably run both versions of the test and add a BIDS filter file to ignore the field maps in the nofmap test.

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I'd rather push that for a separate PR though.

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Just opened #916 for this.

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Expand Up @@ -20,9 +20,7 @@ sub-PNC/anat/sub-PNC_space-ACPC_dseg.nii.gz
sub-PNC/dwi
sub-PNC/dwi/sub-PNC_acq-realistic_desc-confounds_timeseries.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-brain_mask.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.csv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-image_qc.tsv
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.b_table.txt
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.bval
Expand All @@ -31,3 +29,5 @@ sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-preproc_dwi.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_desc-slice_qc.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_dwiref.nii.gz
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-PNC/dwi/sub-PNC_acq-realistic_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
6 changes: 3 additions & 3 deletions qsiprep/tests/data/forrest_gump_outputs.txt
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Expand Up @@ -22,9 +22,7 @@ sub-01/ses-forrestgump/anat/sub-01_ses-forrestgump_rec-autobox_from-orig_to-anat
sub-01/ses-forrestgump/dwi
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_desc-confounds_timeseries.tsv
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-brain_mask.nii.gz
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-image_qc.csv
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-image_qc.tsv
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.b_table.txt
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.bval
Expand All @@ -33,3 +31,5 @@ sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.js
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-preproc_dwi.nii.gz
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_desc-slice_qc.json
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_dwiref.nii.gz
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_model-eddy_stat-cnr_dwimap.json
sub-01/ses-forrestgump/dwi/sub-01_ses-forrestgump_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
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