Add GFA plot.

Author: tsalo

analysis/plot_qsirecon_scalar_maps.py

@@ -14,6 +14,7 @@
     patterns = {
         "DSIStudio GQI FA": "qsirecon-DSIStudioGQI/sub-*/ses-1/dwi/*_space-MNI152NLin2009cAsym_model-tensor_param-fa_dwimap.nii.gz",
         "DSIStudio GQI MD": "qsirecon-DSIStudioGQI/sub-*/ses-1/dwi/*_space-MNI152NLin2009cAsym_model-tensor_param-md_dwimap.nii.gz",
+        "DSIStudio GQI GFA": "qsirecon-DSIStudioGQI/sub-*/ses-1/dwi/*_space-MNI152NLin2009cAsym_model-gqi_param-gfa_dwimap.nii.gz",
     }
     for title, pattern in patterns.items():
         # Get all scalar maps

figures/DSIStudio_GQI_GFA.png

@@ -121,15 +121,6 @@ def run_tedana(raw_dir, fmriprep_dir, aroma_dir, temp_dir, tedana_out_dir):
         )
         assert os.path.isfile(mask), mask
 
-        t2star = os.path.join(
-            fmriprep_dir,
-            subject,
-            "ses-1",
-            "func",
-            f"{mask_base}_part-mag_T2starmap.nii.gz",
-        )
-        assert os.path.isfile(t2star), t2star
-
         # Get the fMRIPrep confounds file and identify the number of non-steady-state volumes
         confounds_file = os.path.join(
             fmriprep_dir,
@@ -154,6 +145,16 @@ def run_tedana(raw_dir, fmriprep_dir, aroma_dir, temp_dir, tedana_out_dir):
 
         # Get the fMRIPost-AROMA mixing file
         mask_base = "_".join([p for p in mask_base.split("_") if not p.startswith("dir")])
+
+        t2star = os.path.join(
+            fmriprep_dir,
+            subject,
+            "ses-1",
+            "func",
+            f"{mask_base}_space-boldref_T2starmap.nii.gz",
+        )
+	assert os.path.isfile(t2star), t2star
+
         mixing = os.path.join(
             aroma_dir,
             subject,

processing/run_tedana.py

@@ -0,0 +1,7 @@
+/var/spool/slurmd/job6025805/slurm_script: line 9: /cbica/projects/pafin/.bashrc: Permission denied
+Run 'mamba init' to be able to run mamba activate/deactivate
+and start a new shell session. Or use conda to activate/deactivate.
+
+  File "/gpfs/fs001/cbica/projects/pafin/code/processing/run_tedana.py", line 156
+    assert os.path.isfile(t2star), t2star
+TabError: inconsistent use of tabs and spaces in indentation