changing output file names and adding stdout messages for clarity

Author: Arshitha

README.md

@@ -77,7 +77,7 @@ for i in `ls -d <path/to/BIDS/input/dataset>*`; do
   done > defacing_parallel_session_level.swarm
 ```
 ```bash
-swarm -f defacing_parallel_subject_level.swarm --module afni,fsl --merge-output --logdir swarm_log
+swarm -f defacing_parallel_session_level.swarm --module afni,fsl --merge-output --logdir swarm_log
 ```
 
 ### Visually inspect defaced scans using VisualQC

src/deface.py

@@ -22,7 +22,7 @@ def rename_afni_workdir(workdir_path):
     new_workdir_path = workdir_path.parent / f'workdir_{default_prefix}'
     workdir_path.rename(new_workdir_path)
 
-    print(f"Removing unwanted files and renaming AFNI workdirs..")
+    print(f"Removing unwanted files and renaming AFNI workdirs..\n")
 
     return new_workdir_path
 

src/dsst_defacing_wf.py

@@ -119,23 +119,24 @@ def generate_3d_renders(defaced_img, render_outdir):
         yaw, pitch, roll = rot[0], rot[1], rot[2]
         outfile = render_outdir.joinpath('defaced_render_' + str(idx) + '.png')
         fsleyes_render_cmd = f"fsleyes render --scene 3d -rot {yaw} {pitch} {roll} --outfile {outfile} {defaced_img} -dr 20 250 -in spline -bf 0.3 -r 100 -ns 500"
+        print(fsleyes_render_cmd)
         run_command(fsleyes_render_cmd)
 
 
-def create_vqc_id_list(vqc_dir):
-    rel_paths_to_orig = [re.sub('/orig.nii.gz', '', str(o.relative_to(vqc_dir))) for o in vqc_dir.rglob('orig.nii.gz')]
-    with open(vqc_dir / 'vqcdeface_id_list.txt', 'w') as f:
+def create_defacing_id_list(qc_dir):
+    rel_paths_to_orig = [re.sub('/orig.nii.gz', '', str(o.relative_to(qc_dir))) for o in qc_dir.rglob('orig.nii.gz')]
+    with open(qc_dir / 'defacing_id_list.txt', 'w') as f:
         f.write('\n'.join(rel_paths_to_orig))
 
 
 def vqcdeface_prep(input_dir, defacing_output_dir):
-    vqcdeface_dir = defacing_output_dir.parent / 'visualqc_prep' / 'vqcdeface'
+    defacing_qc_dir = defacing_output_dir.parent / 'QC_prep' / 'defacing_QC'
     interested_files = [f for f in defacing_output_dir.rglob('*.nii.gz') if
                         'afni_intermediate_files' not in str(f).split('/')]
     for defaced_img in interested_files:
         # please kill me now ughhh
         entities = defaced_img.name.split('.')[0].split('_')
-        vqcd_subj_dir = vqcdeface_dir / f"{'/'.join(entities)}"
+        vqcd_subj_dir = defacing_qc_dir / f"{'/'.join(entities)}"
         vqcd_subj_dir.mkdir(parents=True, exist_ok=True)
 
         defaced_link = vqcd_subj_dir / 'defaced.nii.gz'
@@ -146,9 +147,9 @@ def vqcdeface_prep(input_dir, defacing_output_dir):
         img_link = vqcd_subj_dir / 'orig.nii.gz'
         if not img_link.exists(): img_link.symlink_to(img)
 
-    create_vqc_id_list(vqcdeface_dir)
+    create_defacing_id_list(defacing_qc_dir)
 
-    vqcdeface_cmd = f"vqcdeface -u {vqcdeface_dir} -i {vqcdeface_dir / 'vqcdeface_id_list.txt'} -m orig.nii.gz -d defaced.nii.gz -r defaced_render"
+    vqcdeface_cmd = f"vqcdeface -u {defacing_qc_dir} -i {defacing_qc_dir / 'defacing_id_list.txt'} -m orig.nii.gz -d defaced.nii.gz -r defaced_render"
 
     return vqcdeface_cmd
 
@@ -189,13 +190,15 @@ def main():
         f.write('\n'.join(afni_refacer_failures))  # TODO Not very useful when running the pipeline in parallel
 
     # reorganizing the directory with defaced images into BIDS tree
+    print(f"Reorganizing the directory with defaced images into BIDS tree...\n")
     reorganize_into_bids(input_dir, defacing_outputs, mapping_dict, no_clean)
 
     # prep for visual inspection using visualqc deface
+    print(f"Preparing for QC by visual inspection...\n")
     vqcdeface_cmd = vqcdeface_prep(input_dir, defacing_outputs)
-    print(f"Run the following command to start a VisualQC Deface session:\n{vqcdeface_cmd}")
-    with open(output / 'visualqc_prep' / 'defacing_qc_cmd', 'w') as f:
-        f.write(vqcdeface_cmd)
+    print(f"Run the following command to start a VisualQC Deface session:\n\t{vqcdeface_cmd}\n")
+    with open(output / 'QC_prep' / 'defacing_qc_cmd', 'w') as f:
+        f.write(vqcdeface_cmd + '\n')
 
 
 if __name__ == "__main__":

src/generate_mappings.py

@@ -32,7 +32,7 @@ def run_command(cmdstr, logfile):
     subprocess.run(cmdstr, stdout=logfile, stderr=subprocess.STDOUT, encoding='utf8', shell=True)
 
 
-def primary_scans_qc_prep(mapping_dict, visualqc_prep):
+def primary_scans_qc_prep(mapping_dict, qc_prep):
     """Prepares a directory tree with symbolic links to primary scans and an id_list of primary scans to be used in the
     visualqc_t1_mri command.
 
@@ -57,7 +57,7 @@ def primary_scans_qc_prep(mapping_dict, visualqc_prep):
         # remove empty strings from primaries list
         primaries = [p for p in primaries if p != '']
 
-    vqc_t1_mri = visualqc_prep / 't1_mri'
+    vqc_t1_mri = qc_prep / 't1_mri_QC'
     vqc_t1_mri.mkdir(parents=True, exist_ok=True)
 
     id_list = []
@@ -79,10 +79,10 @@ def primary_scans_qc_prep(mapping_dict, visualqc_prep):
         if not primary_link.exists():
             primary_link.symlink_to(primary)
 
-    with open(visualqc_prep / 'id_list_t1.txt', 'w') as f:
+    with open(vqc_t1_mri / 't1_mri_id_list.txt', 'w') as f:
         f.write('\n'.join([str(i) for i in id_list]))
 
-    vqc_t1_mri_cmd = f"visualqc_t1_mri -u {vqc_t1_mri} -i {vqc_t1_mri.parent / 'vqc_t1_id_list.txt'} -m primary.nii.gz"
+    vqc_t1_mri_cmd = f"visualqc_t1_mri -u {vqc_t1_mri} -i {vqc_t1_mri / 't1_mri_id_list.txt'} -m primary.nii.gz"
 
     return vqc_t1_mri_cmd
 
@@ -203,7 +203,7 @@ def summary_to_stdout(vqc_t1_cmd, sess_ct, t1s_found, t1s_not_found, no_anat_dir
 
 def crawl(input_dir, output):
     # make dir for log files and visualqc prep
-    dir_names = ['logs', 'visualqc_prep']
+    dir_names = ['logs', 'QC_prep']
     for dir_name in dir_names:
         output.joinpath(dir_name).mkdir(parents=True, exist_ok=True)
 
@@ -234,8 +234,8 @@ def crawl(input_dir, output):
         f3.write('\n'.join([str(p) for p in no_anat_dirs]))
 
     # write vqc command to file
-    vqc_t1_mri_cmd = primary_scans_qc_prep(mapping_dict, output / 'visualqc_prep')
-    with open(output / 'visualqc_prep' / 't1_mri_qc_cmd', 'w') as f4:
+    vqc_t1_mri_cmd = primary_scans_qc_prep(mapping_dict, output / 'QC_prep')
+    with open(output / 'QC_prep' / 't1_mri_qc_cmd', 'w') as f4:
         f4.write(f"{vqc_t1_mri_cmd}\n")
 
     summary_to_stdout(vqc_t1_mri_cmd, total_sessions, t1s_found, t1s_not_found, no_anat_dirs, output)

src/register.py

@@ -19,7 +19,7 @@ def preprocess_facemask(fmask_path, logfile_obj):
 
     # arithmetic on the result from above
     c2 = f"fslmaths {prefix}.nii.gz -abs -binv {defacemask}"
-    print(f"Splitting the facemask volume at {fmask_path} and binarizing the resulting volume... \n ")
+    print(f"Generating a defacemask... \n ")
     run_command('; '.join([c0, c1, c2]), logfile_obj)
     try:
         if defacemask.exists():
@@ -59,13 +59,16 @@ def register_to_primary_scan(subj_dir, afni_workdir, primary_scan, other_scans_l
         matrix, reg_out, other_mask, other_defaced = get_intermediate_filenames(other_outdir, other_prefix)
 
         other_outdir.mkdir(parents=True, exist_ok=True)
-        cp_cmd = f"cp {other} {other_outdir.joinpath('original.nii.gz')}"
+        cp_cmd = f"cp {other} {other_outdir / other_prefix}"
 
-        flirt_cmd = f"flirt -dof 6 -cost mutualinfo -searchcost mutualinfo -in {primary_scan} "f"-ref {other} -omat {matrix} -out {reg_out}"
+        flirt_cmd = f"flirt -dof 6 -cost mutualinfo -searchcost mutualinfo -in {primary_scan} -ref {other} -omat {matrix} -out {reg_out}"
 
         # t1 mask can be found in the afni work directory
-        applyxfm_cmd = f"flirt -interp nearestneighbour -applyxfm -init {matrix} "f"-in {t1_mask} -ref {other} -out {other_mask}"
+        applyxfm_cmd = f"flirt -interp nearestneighbour -applyxfm -init {matrix} -in {t1_mask} -ref {other} -out {other_mask}"
 
         mask_cmd = f"fslmaths {other} -mas {other_mask} {other_defaced}"
+
         full_cmd = " ; ".join(["module load fsl", cp_cmd, flirt_cmd, applyxfm_cmd, mask_cmd]) + '\n'
+
+        print(f"Registering {other.name} to {primary_scan.name} and applying defacemask...")
         run_command(full_cmd, log_fileobj)