Minor bugfixes and docfixes

README.md

@@ -36,7 +36,7 @@ Modules (all run by default):
    - outputs a hypothalamic subsegmentation including 3rd ventricle, c. mammilare, fornix and optic tracts.
    - a T1w image is highly recommended ([notes on input images](#requirements-to-input-images)), supports high-res (up to 0.7mm, but experimental beyond that).
    - allows the additional passing of a T2w image with `--t2 <path>`, which will be registered to the T1w image (see `--reg_mode` option).
-   - calculates volume statistics corrected for partial volume effects based on the T1w image (skipped if `--no_biasfield` is passed).
+   - calculates summary statistics based on the biasfield-corrected T1w image (skipped if `--no_biasfield` is passed).
 
 ### Surface reconstruction
 - approximately 60-90 minutes, `--surf_only` runs only [the surface part](recon_surf/README.md).

doc/scripts/RUN_FASTSURFER.md

@@ -40,7 +40,7 @@ Optional arguments
 * `--no_hypothal`: Skip the hypothalamus segmentation.
 * `--no_cc`: Skip the segmentation and analysis of the corpus callosum.
 * `--cereb_segfile`: Name of the cerebellum segmentation file. If not provided, this intermediate DL-based segmentation will not be stored, but only the merged segmentation will be stored (see --main_segfile <filename>). Requires an ABSOLUTE Path! Default location: \$SUBJECTS_DIR/\$sid/mri/cerebellum.CerebNet.nii.gz
-* `--no_biasfield`: Deactivate the biasfield correction and calculation of partial volume-corrected statistics in the segmentation modules.
+* `--no_biasfield`: Deactivate the biasfield correction and calculation of partial volume-corrected statistics in the segmentation modules. HypVINN does run but expects that biasfields are corrected externally.
 * `--native_image` or `--keepgeom`: **Only supported for `--seg_only`**, segment in native image space (keep orientation, image size and voxel size of the input image), this also includes experimental support for anisotropic images (no extreme anisotropy).
 
 ### Surface pipeline arguments

run_fastsurfer.sh

@@ -168,8 +168,8 @@ SEGMENTATION PIPELINE:
                             image will be saved. Requires an ABSOLUTE Path!
                             Default location:
                             \$SUBJECTS_DIR/\$sid/mri/orig.mgz.
-  --no_biasfield          Create a bias field corrected image and enable the
-                            calculation of partial volume-corrected stats-files.
+  --no_biasfield          Deactivate bias field correction and the calculation of
+                            partial volume-corrected stats-files.
   --norm_name <nu.mgz>    Name of the biasfield corrected image
                             Default location:
                             \$SUBJECTS_DIR/\$sid/mri/orig_nu.mgz
@@ -223,11 +223,12 @@ SEGMENTATION PIPELINE:
 
   HYPOTHALAMUS MODULE (HypVINN):
   --no_hypothal           Skip the hypothalamus segmentation.
-  --no_biasfield          This option implies --no_hypothal, 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!
+  --no_biasfield          Biasfield-corrected inputs are recommended for the
+                            hypothalamus sub-segmentation. This option implies images
+                            were corrected externally.
+  --t2 <T2_input>         *Optional* T2 full head input (must be externally biasfield
+                            corrected when called with --no_biasfield). Requires an
+                            ABSOLUTE Path!
   --reg_mode <none|coreg|robust>
                           Ignored, if no T2 image is passed.
                             Specifies the registration method used to register T1
@@ -1045,7 +1046,7 @@ then
       fi
     fi
 
-    if [[ "$run_asegdkt_module" ]]
+    if [[ "$run_asegdkt_module" == "true" ]]
     then
       mask_name_manedit=$(add_file_suffix "$mask_name" "manedit")
       if [[ -e "$mask_name_manedit" ]] ; then mask_name="$mask_name_manedit" ; fi
@@ -1290,7 +1291,7 @@ then
         echo "  with the hypothal module!"
       } | tee -a "$seg_log"
       cmd+=("$t1")
-      if [[ -n "$t2" ]] ; then cmd+=(--t2 "$t2") ; fi
+      if [[ -n "$t2" ]] ; then cmd+=(--t2 "$norm_name_t2") ; fi
     fi
     echo_quoted "${cmd[@]}" | tee -a "$seg_log"
     "${wrap[@]}" "${cmd[@]}" # no tee, directly logging to $seg_log