Merge pull request #50 from Ian-Goodall-Halliwell/main

added 7t compatability

src/functions/constants.py

@@ -62,8 +62,8 @@
 # Resolution
 LOW_RESOLUTION_CTX = "5k"
 HIGH_RESOLUTION_CTX = "32k"
-LOW_RESOLUTION_HIP = "0p5mm"
-HIGH_RESOLUTION_HIP = "2mm"
+LOW_RESOLUTION_HIP = "2mm"
+HIGH_RESOLUTION_HIP = "0p5mm"
 
 map_resolution_ctx = {"low": LOW_RESOLUTION_CTX, "high": HIGH_RESOLUTION_CTX}
 map_resolution_hip = {"low": LOW_RESOLUTION_HIP, "high": HIGH_RESOLUTION_HIP}

src/functions/niidcm.py

@@ -180,7 +180,9 @@ def transfer_nii_hdr_series_tags(ds, nii2dcm_parameters, file_meta):
     ds.PatientName = nii2dcm_parameters["PatientName"]
 
 
-def transfer_nii_hdr_instance_tags(ds, nii2dcm_parameters, instance_index, isbase=False):
+def transfer_nii_hdr_instance_tags(
+    ds, nii2dcm_parameters, instance_index, isbase=False
+):
     """
     Transfer NIfTI header parameters applicable to Instance
 
@@ -289,12 +291,13 @@ def convert_nifti_to_dicom(
     print("NIfTI header series tags transferred.")
     from pydicom.uid import ExplicitVRLittleEndian, ImplicitVRLittleEndian
 
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+
     print("DICOM slices written.")
     if compat == True:
         for i in range(nii2dcm_parameters["NumberOfInstances"]):
-            write_slice_wrapper(
-                (ds, array, i, out_dir, nii2dcm_parameters)
-            )
+            write_slice_wrapper((ds, array, i, out_dir, nii2dcm_parameters))
 
     else:
         useFloat = False

src/functions/run_proc.py

@@ -655,6 +655,31 @@ def run(
                     f"{BIDS_ID}_hemi-{hemi}_space-T1w_den-0p5mm_label-hipp_{surf}.surf.gii",
                 ),
             )
+        shutil.copyfile(
+            os.path.join(
+                subject_micapipe_dir,
+                "xfm",
+                f"{BIDS_ID}_from-nativepro_brain_to-MNI152_0.8mm_mode-image_desc-SyN_0GenericAffine.mat",
+            ),
+            os.path.join(
+                subject_output_dir,
+                "structural",
+                f"{BIDS_ID}_from-nativepro_brain_to-MNI152_0.8mm_mode-image_desc-SyN_0GenericAffine.mat",
+            ),
+        )
+        shutil.copyfile(
+            os.path.join(
+                subject_micapipe_dir,
+                "xfm",
+                f"{BIDS_ID}_from-nativepro_brain_to-MNI152_0.8mm_mode-image_desc-SyN_1Warp.nii.gz",
+            ),
+            os.path.join(
+                subject_output_dir,
+                "structural",
+                f"{BIDS_ID}_from-nativepro_brain_to-MNI152_0.8mm_mode-image_desc-SyN_1Warp.nii.gz",
+            ),
+        )
+
     # do the mapping
     for feat in features:
         if structure == "cortex":

src/functions/surface_to_volume.py

@@ -16,14 +16,14 @@
 settozero = True
 
 
-def fixmatrix(path, subject, session, temppath, wb_path, rootzbrainfolder):
+def fixmatrix(subject, session, temppath, wb_path, rootzbrainfolder):
     # Load the .mat file
     mat = scipy.io.loadmat(
         os.path.join(
-            path,
-            "xfm",
+            rootzbrainfolder,
+            "structural",
             f"{subject}_{session}_from-nativepro_brain_to-MNI152_0.8mm_mode-image_desc-SyN_0GenericAffine.mat",
-        )
+        ),
     )
 
     # Extract variables from the .mat file
@@ -56,15 +56,16 @@ def fixmatrix(path, subject, session, temppath, wb_path, rootzbrainfolder):
         "-convert-warpfield",
         "-from-itk",
         os.path.join(
-            path,
-            "xfm",
+            rootzbrainfolder,
+            "structural",
             f"{subject}_{session}_from-nativepro_brain_to-MNI152_0.8mm_mode-image_desc-SyN_1Warp.nii.gz",
         ),
         "-to-world",
         os.path.join(temppath, "real_warp.nii.gz"),
     ]
-    subprocess.run(command)
-    command3 = [
+    # command = [f'"{arg}"' for arg in command]
+    subprocess.run(" ".join(command), shell=True)
+    command2 = [
         os.path.join(wb_path, "wb_command"),
         "-volume-resample",
         f"{rootzbrainfolder}/structural/{subject}_{session}_space-nativepro_T1w_brain.nii.gz",
@@ -76,7 +77,7 @@ def fixmatrix(path, subject, session, temppath, wb_path, rootzbrainfolder):
         "-warp",
         os.path.join(temppath, "real_warp.nii.gz"),
     ]
-    subprocess.run(command3)
+    subprocess.run(" ".join(command2), shell=True)
     command3 = [
         os.path.join(wb_path, "wb_command"),
         "-volume-resample",
@@ -90,7 +91,7 @@ def fixmatrix(path, subject, session, temppath, wb_path, rootzbrainfolder):
         os.path.join(temppath, "real_warp.nii.gz"),
     ]
 
-    subprocess.run(command3)
+    subprocess.run(" ".join(command3), shell=True)
 
 
 def float_array_to_hot_nonrgb(array):
@@ -1054,7 +1055,7 @@ def surface_to_volume(
     # dicomify_base(outdir, rootzbrainfolder, subj=subj, ses=ses, px_demo=px_demo)
 
     micapiperootfolder = os.path.join(rootfolder, micapipename, subj, ses)
-    fixmatrix(micapiperootfolder, subj, ses, tmp, workbench_path, rootzbrainfolder)
+    fixmatrix(subj, ses, tmp, workbench_path, rootzbrainfolder)
     Parallel(n_jobs=n_jobs)(
         delayed(process)(
             feature,
@@ -1103,7 +1104,7 @@ def surface_to_volume(
     )
     if dicoms == 1:
         os.makedirs(f"{outdir}/DICOM", exist_ok=True)
-        dicomify_base(outdir, subj, ses, tmp, thresh, px_demo=px_demo)
+        dicomify_base(outdir, rootzbrainfolder, subj, ses, px_demo=px_demo)
         print("Converting to DICOM")
         timepre = time()
         Parallel(n_jobs=n_jobs)(

src/zbrains.py

@@ -523,9 +523,10 @@ def check_sub(args, sub, ses=None):
             hippunfold_path = os.path.join(hippunfold_path, ses)
     if not os.path.isdir(micapipe_path):
         # print(f'Non proccessable micapipe output at {micapipe_path} for {sub}{f"-{ses}" if ses else ""}, skipping')
-        return False
+        if "proc" in args.run:
+            return False
     if "proc" in args.run:
-        
+
         if "cortex" in args.struct or "subcortex" in args.struct:
             if not os.path.exists(micapipe_path) or not os.path.isdir(micapipe_path):
                 print(
@@ -540,7 +541,6 @@ def check_sub(args, sub, ses=None):
                     f'No hippunfold at {hippunfold_path} for {sub}{f"-{ses}" if ses else ""}, skipping'
                 )
                 return False
-
 
     return True
 
@@ -560,7 +560,7 @@ def create_jobs(args, subs, ses, run_type):
             if check_sub(args, sub, s):
                 job = copy.copy(args)
                 job.sub, job.ses, job.run = sub, s, run_type
-                if args.patient_prefix in job.sub or run_type == "proc":
+                if args.control_prefix not in job.sub or run_type == "proc":
                     jobs.append(job)
     return jobs
 
@@ -714,7 +714,7 @@ def print_help(self):
         type=str,
         default="/data/mica1/01_programs/workbench-1.4.2/bin_linux64",
     )
-    parser.add_argument("--patient_prefix", type=str, default="PX")
+    parser.add_argument("--control_prefix", type=str, default="HC")
     parser.add_argument("--verbose", type=int, default=-1)
     parser.add_argument("--version", action="version", version="1.0.0")
     parser.add_argument("--dicoms", type=int, default=1)