Update QSIRecon figures.

Author: tsalo

analysis/plot_qsirecon_scalar_maps.py

@@ -12,8 +12,6 @@
     out_dir = "../figures"
 
     patterns = {
-        "NODDI ICVF": "qsirecon-wmNODDI/sub-*/ses-1/dwi/*_space-MNI152NLin2009cAsym_model-noddi_param-icvf_dwimap.nii.gz",
-        "TORTOISE RTOP": "qsirecon-TORTOISE_model-MAPMRI/sub-*/ses-1/dwi/*_space-MNI152NLin2009cAsym_model-mapmri_param-rtop_dwimap.nii.gz",
         "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",
     }

figures/DSIStudio_GQI_FA.png

@@ -121,6 +121,15 @@ 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,
@@ -208,6 +217,7 @@ def run_tedana(raw_dir, fmriprep_dir, aroma_dir, temp_dir, tedana_out_dir):
             mixm=mixing2,
             gscontrol=["mir"],
             tedort=True,
+            t2smap=t2star,
         )
 
 

figures/DSIStudio_GQI_MD.png

@@ -0,0 +1,13 @@
+/var/spool/slurmd/job6025568/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.
+
+TEDANA
+	sub-24053_ses-1_task-bao_dir-AP_run-01_echo-1_part-mag_bold.nii.gz
+Traceback (most recent call last):
+  File "/gpfs/fs001/cbica/projects/pafin/code/processing/run_tedana.py", line 405, in <module>
+    run_tedana(raw_dir_, fmriprep_dir_, aroma_dir_, temp_dir_, tedana_out_dir_)
+  File "/gpfs/fs001/cbica/projects/pafin/code/processing/run_tedana.py", line 131, in run_tedana
+    assert os.path.isfile(t2star), t2star
+           ^^^^^^^^^^^^^^^^^^^^^^
+AssertionError: /cbica/projects/pafin/derivatives/fmriprep/sub-24053/ses-1/func/sub-24053_ses-1_task-bao_dir-AP_run-01_part-mag_T2starmap.nii.gz