Set output directory for derivative datasinks (#914)

* Fix datasinks?

* Change topupcsv filename.

* Update tortoise.py

* Update filenames in .circleci too.

* Update preprocessing.rst

.circleci/DSCSDSI_outputs.txt

@@ -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

.circleci/DSDTI_nofmap_outputs.txt

@@ -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

.circleci/DSDTI_outputs.txt

@@ -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

.circleci/DSDTI_synsdc_outputs.txt

@@ -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

.circleci/IntramodalTemplate_outputs.txt

@@ -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
@@ -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

docs/preprocessing.rst

@@ -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

qsiprep/data/io_spec.json

@@ -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}",

qsiprep/interfaces/eddy.py

@@ -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()
@@ -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,
@@ -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
 

qsiprep/interfaces/epi_fmap.py

@@ -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(
@@ -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'],
     )

qsiprep/interfaces/reports.py

@@ -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
 

qsiprep/interfaces/tortoise.py

@@ -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,
@@ -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]

qsiprep/tests/data/drbuddi_rpe_outputs.txt

@@ -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
@@ -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

qsiprep/tests/data/drbuddi_shoreline_epi_outputs.txt

@@ -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
@@ -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

qsiprep/tests/data/drbuddi_tensorline_epi_outputs.txt

@@ -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

qsiprep/tests/data/dscsdsi_outputs.txt

@@ -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
@@ -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

qsiprep/tests/data/dsdti_nofmap_outputs.txt

@@ -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
@@ -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

qsiprep/tests/data/dsdti_synfmap_outputs.txt

@@ -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
@@ -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

qsiprep/tests/data/dsdti_topup_outputs.txt

@@ -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
@@ -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

qsiprep/tests/data/forrest_gump_outputs.txt

@@ -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
@@ -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