Merge branch 'main' into fix-connectivity-fields

PennLINC · Nov 19, 2024 · eaf5705 · eaf5705
2 parents 77de336 + 64be9d6
commit eaf5705
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Showing 5 changed files with 26 additions and 5 deletions.
diff --git a/qsirecon/cli/recon_plot.py b/qsirecon/cli/recon_plot.py
@@ -101,6 +101,7 @@ def recon_plot():
     parser.add_argument("--padding", type=int, default=10, help="number of slices to plot")
     opts = parser.parse_args()
 
+    print(f"TMPDIR={os.getenv('TMPDIR')}")
     if opts.mif:
         odf_img, directions = mif2amps(opts.mif, os.getcwd())
         LOGGER.info("converting %s to plot ODF/peaks", opts.mif)

diff --git a/qsirecon/workflows/recon/amico.py b/qsirecon/workflows/recon/amico.py
@@ -125,7 +125,11 @@ def init_amico_noddi_fit_wf(
     ])  # fmt:skip
 
     if plot_reports:
-        plot_peaks = pe.Node(CLIReconPeaksReport(), name="plot_peaks", n_procs=omp_nthreads)
+        plot_peaks = pe.Node(
+            CLIReconPeaksReport(environ={"TMPDIR": str(config.execution.work_dir)}),
+            name="plot_peaks",
+            n_procs=omp_nthreads,
+        )
         ds_report_peaks = pe.Node(
             DerivativesDataSink(
                 datatype="figures",

diff --git a/qsirecon/workflows/recon/dipy.py b/qsirecon/workflows/recon/dipy.py
@@ -189,7 +189,11 @@ def init_dipy_brainsuite_shore_recon_wf(
     ])  # fmt:skip
 
     if plot_reports:
-        plot_peaks = pe.Node(CLIReconPeaksReport(), name="plot_peaks", n_procs=omp_nthreads)
+        plot_peaks = pe.Node(
+            CLIReconPeaksReport(environ={"TMPDIR": str(config.execution.work_dir)}),
+            name="plot_peaks",
+            n_procs=omp_nthreads,
+        )
         ds_report_peaks = pe.Node(
             DerivativesDataSink(
                 desc="3dSHOREODF",
@@ -495,7 +499,11 @@ def init_dipy_mapmri_recon_wf(
     ])  # fmt:skip
 
     if plot_reports:
-        plot_peaks = pe.Node(CLIReconPeaksReport(), name="plot_peaks", n_procs=omp_nthreads)
+        plot_peaks = pe.Node(
+            CLIReconPeaksReport(environ={"TMPDIR": str(config.execution.work_dir)}),
+            name="plot_peaks",
+            n_procs=omp_nthreads,
+        )
         ds_report_peaks = pe.Node(
             DerivativesDataSink(
                 desc="MAPLMRIODF",

diff --git a/qsirecon/workflows/recon/dsi_studio.py b/qsirecon/workflows/recon/dsi_studio.py
@@ -104,7 +104,11 @@ def init_dsi_studio_recon_wf(inputs_dict, name="dsi_studio_recon", qsirecon_suff
     if plot_reports:
         # Make a visual report of the model
         plot_peaks = pe.Node(
-            CLIReconPeaksReport(subtract_iso=True), name="plot_peaks", n_procs=omp_nthreads
+            CLIReconPeaksReport(
+                environ={"TMPDIR": str(config.execution.work_dir)}, subtract_iso=True
+            ),
+            name="plot_peaks",
+            n_procs=omp_nthreads,
         )
         ds_report_peaks = pe.Node(
             DerivativesDataSink(

diff --git a/qsirecon/workflows/recon/mrtrix.py b/qsirecon/workflows/recon/mrtrix.py
@@ -239,7 +239,11 @@ def init_mrtrix_csd_recon_wf(inputs_dict, name="mrtrix_recon", qsirecon_suffix="
 
     if not config.execution.skip_odf_reports:
         # Make a visual report of the model
-        plot_peaks = pe.Node(CLIReconPeaksReport(), name="plot_peaks", n_procs=omp_nthreads)
+        plot_peaks = pe.Node(
+            CLIReconPeaksReport(environ={"TMPDIR": str(config.execution.work_dir)}),
+            name="plot_peaks",
+            n_procs=omp_nthreads,
+        )
         ds_report_peaks = pe.Node(
             DerivativesDataSink(
                 desc="wmFOD",