update run_fastsurfer.sh for hypvinn

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Deep-MI · Apr 18, 2024 · f71d2fe · f71d2fe
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diff --git a/FastSurferCNN/models/networks.py b/FastSurferCNN/models/networks.py
@@ -13,17 +13,17 @@
 # limitations under the License.
 
 # IMPORTS
-from typing import Optional
+from typing import Optional, TYPE_CHECKING
 
 import numpy as np
-import yacs.config
 from torch import Tensor, nn
+if TYPE_CHECKING:
+    import yacs.config
 
 import FastSurferCNN.models.interpolation_layer as il
 import FastSurferCNN.models.sub_module as sm
 
 
-
 class FastSurferCNNBase(nn.Module):
     """
     Network Definition of Fully Competitive Network network.
@@ -387,7 +387,7 @@ def forward(
 }
 
 
-def build_model(cfg: yacs.config.CfgNode) -> FastSurferCNN | FastSurferVINN:
+def build_model(cfg: 'yacs.config.CfgNode') -> FastSurferCNN | FastSurferVINN:
     """
     Build requested model.
 

diff --git a/HypVINN/README.md b/HypVINN/README.md
@@ -27,7 +27,7 @@ Run the HypVINN/run_pipeline.py which has the following arguments:
  * `--seg_log` :  Path to file in which run logs will be saved. If not set logs will be stored in /sd/sid/logs/hypvinn_seg.log 
 ### Image processing options
  * `--no_reg` : Deactivate registration of T2 to T1. If multi modal input is used; images need to be registered externally,
- * `--reg_type` : Freesurfer Registration type to run. coreg : mri_coreg (Default) or robust : mri_robust_register.
+ * `--reg_mode` : Freesurfer Registration type to run. coreg : mri_coreg (Default) or robust : mri_robust_register.
  * `--qc_snap`: Activate the creation of QC snapshots of the predicted HypVINN segmentation.
 ###  FastSurfer Technical parameters (see FastSurfer documentation)
  * `--device`
@@ -57,15 +57,15 @@ The pipeline can do all pre-processing by itself (step 1). This step can be skip
     python HypVINN/run_pipeline.py  --sid test_subject --sd /output \
                                      --t1 /data/test_subject_t1.nii.gz \
                                      --t2 /data/test_subject_t2.nii.gz \
-                                     --reg_type coreg \
+                                     --reg_mode coreg \
                                      --seg_log /outdir/test_subject.log \
                                      --batch_size 6
    ```
 2. Run full pipeline only using a t1 
     ```
     python HypVINN/run_pipeline.py  --sid test_subject --sd /output \
                                      --t1 /data/test_subject_t1.nii.gz \
-                                     --reg_type coreg \
+                                     --reg_mode coreg \
                                      --seg_log /outdir/test_subject.log \
                                      --batch_size 6
    ```
@@ -75,7 +75,7 @@ The pipeline can do all pre-processing by itself (step 1). This step can be skip
     python HypVINN/run_pipeline.py  --sid test_subject --sd /output \
                                      --t1 /data/test_subject_t1.nii.gz \
                                      --t2 /data/test_subject_t2.nii.gz \
-                                     --reg_type coreg \
+                                     --reg_mode coreg \
                                      --seg_log /outdir/test_subject.log \
                                      --batch_size 6 --no_reg
    ```
@@ -85,7 +85,7 @@ The pipeline can do all pre-processing by itself (step 1). This step can be skip
     python HypVINN/run_pipeline.py  --sid test_subject --sd /output \
                                      --t1 /data/test_subject_t1.nii.gz \
                                      --t2 /data/test_subject_t2.nii.gz \
-                                     --reg_type coreg \
+                                     --reg_mode coreg \
                                      --seg_log /outdir/test_subject.log \
                                      --batch_size 6 --qc_snap
    ```

diff --git a/HypVINN/run_pipeline.py b/HypVINN/run_pipeline.py
@@ -42,18 +42,31 @@ def option_parse():
     parser = parser_defaults.add_arguments(
         parser, ["t1"]
     )
-
-    parser.add_argument('--t2', type=lambda x : None if x == 'None' else str(x), default=None,required=False, help="path to the T2 image to process")
+    parser.add_argument(
+        '--t2',
+        type=lambda x : None if x == 'None' else str(x),
+        default=None,
+        required=False,
+        help="Path to the T2 image to process.",
+    )
 
     # 3. Image processing options
-    parser.add_argument("--no_reg", action='store_false', dest="registration", help="Deactivate registration of T2 to t1,"
-                                                                                    "If multi mode is run images need to be register properly")
-
-    parser.add_argument("--qc_snap", action='store_true', dest="qc_snapshots",
-                        help="Create qc snapshots")
-
-    parser.add_argument('--reg_type', type=str, default="coreg", choices=["coreg", "robust"],
-                        help="Freesurfer Registration type to run. coreg: mri_coreg, robust : mri_robust_register  ")
+    parser.add_argument(
+        "--qc_snap",
+        action='store_true',
+        dest="qc_snapshots",
+        help="Create qc snapshots",
+    )
+    parser.add_argument(
+        "--reg_mode",
+        type=str,
+        default="coreg",
+        choices=["none", "coreg", "robust"],
+        help="Freesurfer Registration type to run. coreg: mri_coreg, "
+             "robust : mri_robust_register, none: entirely deactivates "
+             "registration of T2 to T1, if both images are passed, "
+             "images need to be register properly externally.",
+    )
 
 
 

diff --git a/HypVINN/utils/preproc.py b/HypVINN/utils/preproc.py
@@ -93,7 +93,7 @@ def hyvinn_preproc(args):
 
             LOGGER.info("Registering T1 to T2 ...")
             args.t2 = t1_to_t2_registration(t1_path=args.t1, t2_path=args.t2, out_dir=args.out_dir,
-                                               registration_type=args.reg_type)
+                                               registration_type=args.reg_mode)
             LOGGER.info("Registration finish in {:0.4f} seconds".format(time.time() - load_res))
         else:
             LOGGER.info(

diff --git a/recon_surf/N4_bias_correct.py b/recon_surf/N4_bias_correct.py
@@ -651,7 +651,6 @@ def main (options):
 
 
 if __name__ == "__main__":
-
     # Command Line options are error checking done here
     options = options_parse()
     sys.exit(main(options))
diff --git a/run_fastsurfer.sh b/run_fastsurfer.sh
@@ -37,14 +37,17 @@ reconsurfdir="$FASTSURFER_HOME/recon_surf"
 # Regular flags defaults
 subject=""
 t1=""
-# TODO include <T2_input>
+t2=""
 merged_segfile=""
 cereb_segfile=""
 asegdkt_segfile=""
 asegdkt_segfile_default="\$SUBJECTS_DIR/\$SID/mri/aparc.DKTatlas+aseg.deep.mgz"
 asegdkt_statsfile=""
 cereb_statsfile=""
 cereb_flags=()
+hypo_segfile=""
+hypo_statsfile=""
+hypvinn_flags=()
 conformed_name=""
 seg_log=""
 run_talairach_registration="false"
@@ -59,7 +62,7 @@ surf_flags=()
 vox_size="min"
 run_asegdkt_module="1"
 run_cereb_module="1"
-# TODO include <run_hypvinn_module>
+run_hypvinn_module="1"
 threads="1"
 # python3.10 -s excludes user-directory package inclusion
 python="python3.10 -s"
@@ -185,6 +188,23 @@ SEGMENTATION PIPELINE:
   --no_biasfield          Deactivate the calculation of partial volume-corrected
                             statistics.
 
+  HYPOTHALAMUS MODULE (HypVINN):
+  --no_hypvinn            Skip the hypothalamus segmentation.
+  --no_biasfield          This option implies --no_hypvinn, as the hypothalamus
+                            sub-segmentation requires biasfield-corrected images.
+  --t2 <T2_input>         *Optional* T2 full head input (does not have to be bias
+                            corrected, a mandatory biasfield correction step is
+                            performed). Requires an ABSOLUTE Path!
+  --reg_mode <none|coreg|robust>
+                          Ignored, if no T2 image is passed.
+                            Specifies the registration method used to register T1
+                            and T2 images. Options are 'coreg' (default) for
+                            mri_coreg, 'robust' for mri_robust_register, and 'none'
+                            to skip registration (this requires T1 and T2 are
+                            externally co-registered).
+  --qc_snap               Create QC snapshots in \$SUBJECTS_DIR/\$sid/qc_snapshots
+                            to simplify the QC process.
+
 SURFACE PIPELINE:
   --surf_only             Run surface pipeline only. The segmentation input has
                             to exist already in this case.
@@ -246,15 +266,17 @@ Henschel L*, Kuegler D*, Reuter M. (*co-first). FastSurferVINN: Building
  for HighRes Brain MRI. NeuroImage 251 (2022), 118933. 
  http://dx.doi.org/10.1016/j.neuroimage.2022.118933
 
+For cerebellum sub-segmentation:
 Faber J*, Kuegler D*, Bahrami E*, et al. (*co-first). CerebNet: A fast and
  reliable deep-learning pipeline for detailed cerebellum sub-segmentation.
  NeuroImage 264 (2022), 119703.
  https://doi.org/10.1016/j.neuroimage.2022.119703
 
-Estrada S, Kuegler D, Bahrami E, Xu P, Mousa D, Breteler MMB, Aziz NA, Reuter M. FastSurfer-HypVINN:
-Automated sub-segmentation of the hypothalamus and adjacent structures on high-resolutional brain MRI.
-Imaging Neuroscience 2023; 1 1–32.
-https://doi.org/10.1162/imag_a_00034
+For hypothalamus sub-segemntation:
+Estrada S, Kuegler D, Bahrami E, Xu P, Mousa D, Breteler MMB, Aziz NA, Reuter M.
+ FastSurfer-HypVINN: Automated sub-segmentation of the hypothalamus and adjacent
+ structures on high-resolutional brain MRI. Imaging Neuroscience 2023; 1 1–32.
+ https://doi.org/10.1162/imag_a_00034
 
 EOF
 }
@@ -301,6 +323,11 @@ case $key in
     shift # past argument
     shift # past value
     ;;
+    --t2)
+    t2="$2"
+    shift # past argument
+    shift # past value
+    ;;
     --merged_segfile)
     merged_segfile="$2"
     shift # past argument
@@ -334,6 +361,26 @@ case $key in
     shift # past argument
     shift # past value
     ;;
+    --hypo_segfile)
+    hypo_segfile="$2"
+    shift # past argument
+    shift # past value
+    ;;
+    --hypo_statsfile)
+    hypo_statsfile="$2"
+    shift # past argument
+    shift # past value
+    ;;
+    --reg_mode)
+    mode=$(echo "$2" | tr "[:upper:]" "[:lower:]")
+    if [[ "$mode" =~ /^(none|coreg|robust)$/ ]] ; then
+      hypvinn_flags=("${hypvinn_flags[@]}" --regmode "$mode")
+    else
+      echo "Invalid --reg_mode option, must be 'none', 'coreg' or 'robust'."
+    fi
+    shift # past argument
+    shift # past value
+    ;;
     --mask_name)
     mask_name="$2"
     shift # past argument
@@ -400,6 +447,10 @@ case $key in
     run_cereb_module="0"
     shift  # past argument
     ;;
+    --no_hypvinn)
+    run_hypvinn_module="0"
+    shift  # past argument
+    ;;
     --tal_reg)
     run_talairach_registration="true"
     shift