Respond to review

Author: Andy Worth

README.md

@@ -60,7 +60,7 @@ There are [three ways](https://docs.flywheel.io/hc/en-us/articles/360013235453-H
 
 Generates an automated segmentation of the hippocampal subfields based on a statistical atlas built primarily upon ultra-high resolution (~0.1 mm isotropic) ex vivo MRI data. See: [https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala](https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) for more info.  Choosing this option will write `<subject_id>_HippocampalSubfields.csv` to the final results.  The values in this spreadsheet will also be attached to the analysis as "Custom Information" ("info" metadata) so they can be found using search and in views.  (Default=true)
 
-### gear-thalamic-nuclei (optional)
+### gear-thalamic_nuclei (optional)
 
 Produce a parcellation of the thalamus into 25 different nuclei, using a probabilistic atlas built with histological data. Choosing this option will produce 3 files in the subject's mri directory: `ThalamicNuclei.v12.T1.volumes.txt`, `ThalamicNuclei.v12.T1.mgz`, and `ThalamicNuclei.v12.T1.FSvoxelSpace.mgz`, and 2 files in the stats directory: `thalamic-nuclei.lh.v12.T1.stats` and `thalamic-nuclei.rh.v12.T1.stats`. See: [https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei](https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei) for more info. (Default=false)
 

manifest.json

@@ -2,12 +2,12 @@
   "name": "freesurfer-recon-all",
   "label": "FreeSurfer 7.1.1: run recon-all",
   "description": "FreeSurfer version 7.1.1 Release (July 27, 2020). This gear takes an anatomical NIfTI file and performs all of the FreeSurfer cortical reconstruction process. Outputs are provided in a zip file and include the entire output directory tree from Recon-All. Configuration options exist for setting the subject ID and for converting outputs to NIfTI, OBJ, and CSV. FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. Please see https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense for license information.",
-  "version": "1.0.8_7.1.1",
+  "version": "1.0.9_7.1.1",
   "custom": {
-    "docker-image": "flywheel/freesurfer-recon-all:1.0.8_7.1.1",
+    "docker-image": "flywheel/freesurfer-recon-all:1.0.9_7.1.1",
     "gear-builder": {
       "category": "analysis",
-      "image": "flywheel/freesurfer-recon-all:1.0.8_7.1.1"
+      "image": "flywheel/freesurfer-recon-all:1.0.9_7.1.1"
     },
     "flywheel": {
       "suite": "FreeSurfer"
@@ -86,7 +86,7 @@
       "optional": true
     },
     "expert": {
-      "description": "A user-created file containing special options to include in the command string. The file should contain as the first item the name of the command, and the items following it on rest of the line will be passed as the extra options.",
+      "description": "A user-created file containing special options to include in the command string. The file should contain as the first item the name of the command, and the items following it on rest of the line will be passed as the extra options.  See Freesurfer documentation https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile for more information and examples.",
       "base": "file",
       "optional": true
     }
@@ -128,7 +128,7 @@
       "default": true,
       "type": "boolean"
     },
-    "gear-thalamic-nuclei": {
+    "gear-thalamic_nuclei": {
       "description": "Produce a parcellation of the thalamus into 25 different nuclei, using a probabilistic atlas built with histological data. Choosing this option will produce 3 files in the subject's mri directory: ThalamicNuclei.v12.T1.volumes.txt, ThalamicNuclei.v12.T1.mgz, and ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, and 2 files in the stats directory: thalamic-nuclei.lh.v12.T1.stats and thalamic-nuclei.rh.v12.T1.stats. See: https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei for more info. (Default=false)",
       "default": false,
       "type": "boolean"

run.py

@@ -515,7 +515,7 @@ def do_gear_convert_volumes(config, mri_dir, dry_run, environ, log):
         mri_mgz_files += ["brainstemSsLabels.v12.FSvoxelSpace.mgz"]
     if config.get("gear-gtmseg"):
         mri_mgz_files += ["gtmseg.mgz"]
-    if config.get("gear-thalamic-nuclei"):
+    if config.get("gear-thalamic_nuclei"):
         mri_mgz_files += [
             "ThalamicNuclei.v12.T1.mgz",
             "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz",
@@ -751,7 +751,7 @@ def main(gtk_context):
                         subject_id, mri_dir, dry_run, environ, metadata, log
                     )
 
-                if config.get("gear-thalamic-nuclei"):
+                if config.get("gear-thalamic_nuclei"):
                     do_gear_thalamic_nuclei(
                         subject_id, mri_dir, dry_run, environ, metadata, log
                     )