childmindresearch · nx10 · Dec 2, 2024 · Nov 28, 2024 · Nov 29, 2024 · Nov 29, 2024
diff --git a/descriptors/afni/MBA.json b/descriptors/afni/MBA.json
@@ -5,7 +5,7 @@
   "descriptor-url": "https://github.com/afni/mba_descriptor.json",
   "description": "Matrix-Based Analysis Program through Bayesian Multilevel Modeling",
   "url": "https://afni.nimh.nih.gov/",
-  "command-line": "MBA [PREFIX] [CHAINS] [ITERATIONS] [MODEL] [EOI] [DATA_TABLE] [CVARS] [QVARS] [QCVAR] [STDZ] [WCP] [DISTY] [SE] [RPREFIX] [DBGARGS] [HELP]",
+  "command-line": "MBA [PREFIX] [CHAINS] [ITERATIONS] [MODEL] [EOI] [DATA_TABLE] [CVARS] [QVARS] [QCVAR] [STDZ] [WCP] [DISTY] [SE] [DBGARGS] [HELP]",
   "container-image": {
     "type": "docker",
     "image": "afni/afni_make_build:AFNI_24.2.06"

diff --git a/descriptors/afni/Vecwarp.json b/descriptors/afni/Vecwarp.json
@@ -3,7 +3,7 @@
   "name": "Vecwarp",
   "author": "AFNI Developers",
   "description": "Transforms (warps) a list of 3-vectors into another list of 3-vectors according to the specified options.",
-  "command-line": "Vecwarp [APAR | MATVEC] [FORWARD_FLAG | BACKWARD_FLAG] [INPUT] [OUTPUT] [FORCE]",
+  "command-line": "Vecwarp [APAR] [MATVEC] [FORWARD] [BACKWARD] [INPUT] [OUTPUT] [FORCE]",
   "inputs": [
     {
       "command-line-flag": "-apar",

diff --git a/descriptors/afni/quotize.json b/descriptors/afni/quotize.json
@@ -3,7 +3,7 @@
   "name": "quotize",
   "author": "AFNI Developers",
   "description": "Turns a text file into a C array of strings initialized into an array 'char *name[]'.",
-  "command-line": "quotize [NAME] < [INPUT_FILE] > [OUTPUT_FILE]",
+  "command-line": "quotize [NAME] [INPUT_FILE] [OUTPUT_FILE]",
   "inputs": [
     {
       "description": "The name to be used for the array of strings.",

diff --git a/descriptors/freesurfer/dmrirc.example.json b/descriptors/freesurfer/dmrirc.example.json
diff --git a/descriptors/freesurfer/dmrirc.long.example.json b/descriptors/freesurfer/dmrirc.long.example.json
diff --git a/descriptors/freesurfer/dmrirc.long.multiscan.example.json b/descriptors/freesurfer/dmrirc.long.multiscan.example.json
diff --git a/descriptors/freesurfer/dmrirc.multiscan.example.json b/descriptors/freesurfer/dmrirc.multiscan.example.json
diff --git a/descriptors/freesurfer/mri_ca_normalize.json b/descriptors/freesurfer/mri_ca_normalize.json
@@ -4,7 +4,7 @@
   "author": "FreeSurfer Developers",
   "descriptor-url": "UNKNOWN",
   "description": "This program creates a normalized volume using the brain volume and an input gca file.",
-  "command-line": "mri_ca_normalize [INPUT_BRAIN_VOLUMES] [ATLAS_FILE] [XFORM_FILE] [OUTPUT_VOLUMES] [SEG_FILE] [SIGMA_VALUE] [FSAMPLES_FILE] [DILATE_ITERS] [NSAMPLES_FILE] [MASK_VOL] [CONTROL_POINTS_FILE] [FONLY_FILE] [DIAG_FILE] [DEBUG_VOXEL_COORDS] [DEBUG_NODE_COORDS] [TR_VALUE] [TE_VALUE] [ALPHA_VALUE] [EXAMPLE_MRI_VOL] [EXAMPLE_SEG] [NOVAR_FLAG] [RENORM_FILE] [EXTRA_NORM_PCTL] [FLASH_FLAG] [PRIOR_THRESHOLD] [WRITE_FLAG] [N_REGIONS] [VERBOSE_VALUE] [TOP_PERCENT]",
+  "command-line": "mri_ca_normalize [INPUT_BRAIN_VOLUMES] [ATLAS_FILE] [XFORM_FILE] [OUTPUT_VOLUMES] [SEG_FILE] [SIGMA_VALUE] [FSAMPLES_FILE] [DILATE_ITERS] [NSAMPLES_FILE] [MASK_VOL] [CONTROL_POINTS_FILE] [FONLY_FILE] [DIAG_FILE] [DEBUG_VOXEL_COORDS] [DEBUG_NODE_COORDS] [TR_VALUE] [TE_VALUE] [ALPHA_VALUE] [EXAMPLE_MRI_VOL] [EXTRA_NORM_PCTL] [PRIOR_THRESHOLD] [N_REGIONS] [VERBOSE_VALUE] [TOP_PERCENT] [NOVAR_FLAG] [RENORM_FILE] [FLASH_FLAG]",
   "container-image": {
     "type": "docker",
     "image": "freesurfer/freesurfer:7.4.1"

diff --git a/descriptors/freesurfer/mri_compile_edits.json b/descriptors/freesurfer/mri_compile_edits.json
@@ -1,7 +1,7 @@
 {
   "name": "mri_compile_edits",
   "description": "Program to create a single volume showing all the volumetric edits made to a subject.",
-  "command-line": "mri_compile_edits [OPTIONS] [SUBJECT_NAME] [OUTPUT_VOLUME]",
+  "command-line": "mri_compile_edits [SUBJECT_NAME] [OUTPUT_VOLUME]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_concat.json b/descriptors/freesurfer/mri_concat.json
@@ -3,7 +3,7 @@
   "name": "mri_concat",
   "author": "FreeSurfer Developers",
   "description": "Concatenates input data sets.",
-  "command-line": "mri_concat [INPUT_FILES] [OUTPUT_FILE] [ADDITIONAL_OPTIONS]",
+  "command-line": "mri_concat [INPUT_FILES] [OUTPUT_FILE] [FILE_LIST] [PAIRED_SUM] [PAIRED_AVG] [PAIRED_DIFF] [PAIRED_DIFF_NORM] [PAIRED_DIFF_NORM1] [PAIRED_DIFF_NORM2] [NORM_MEAN] [NORM1] [MATRIX] [FRAME_WEIGHT] [NORM_WEIGHT] [GROUP_MEAN] [COMBINE] [KEEP_DATATYPE] [ABS] [POS] [NEG] [MEAN] [MEDIAN] [MEAN_DIV_N] [SUM] [VAR] [STD] [MAX] [MAX_INDEX] [MAX_INDEX_PRUNE] [MAX_INDEX_ADD] [MIN] [REPLICATE_TIMES] [FNORM] [CONJUNCTION] [VOTE] [SORT] [TEMPORAL_AR1] [PRUNE] [PCA] [PCA_MASK] [SCM] [ZCONCAT] [MAX_BONFCOR] [MULTIPLY] [ADD] [MASK_FILE] [RMS] [NO_CHECK]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_cor2label.json b/descriptors/freesurfer/mri_cor2label.json
@@ -2,7 +2,7 @@
   "name": "mri_cor2label",
   "tool-version": "7.4.1",
   "description": "Converts values in a volume or surface overlay to a label. Designed to convert parcellation volumes stored in mri format.",
-  "command-line": "mri_cor2label -[INPUT_FILE] -[LABEL_ID] -[LABEL_FILE] [THRESHOLD] [VOLUME_FILE] [SURFACE_OVERLAY] [SURFACE_PATH] [OPTIMIZE] [REMOVE_HOLES_ISLANDS] [DILATE] [ERODE] [HELP]",
+  "command-line": "mri_cor2label [INPUT_FILE] [LABEL_ID] [LABEL_FILE] [THRESHOLD] [VOLUME_FILE] [SURFACE_OVERLAY] [SURFACE_PATH] [OPTIMIZE] [REMOVE_HOLES_ISLANDS] [DILATE] [ERODE] [HELP]",
   "container-image": {
     "type": "docker",
     "image": "freesurfer/freesurfer:7.4.1"

diff --git a/descriptors/freesurfer/mri_coreg.json b/descriptors/freesurfer/mri_coreg.json
@@ -4,7 +4,7 @@
   "author": "FreeSurfer Developers",
   "descriptor-url": "https://github.com/freesurfer/freesurfer/blob/dev/mri_coreg/cbsd.json",
   "description": "mri_coreg performs a linear registration between two volumes using the method compatible with spm_coreg.",
-  "command-line": "mri_coreg -[MOVVOL] -[REFVOL] -[REG] [ADDITIONAL_PARAMETERS]",
+  "command-line": "mri_coreg [MOVVOL] [REFVOL] [REG] [SUBJECT] [DOF] [ZSCALE] [XZTRANS_YROT] [XYTRANS_ZROT] [XYTRANS_ZROT_XYSCALE_XYSHEAR] [REF_MASKVOL] [NO_REF_MASK] [MOV_MASKVOL] [THREADS] [SUBJECTS_DIR] [REGDAT] [NO_COORD_DITHER] [NO_INTENSITY_DITHER] [SPATIAL_SCALES] [TRANS] [ROT] [SCALE] [SHEAR] [INIT_REG] [OUT_PARAM_FILE] [OUT_COST_FILE] [NO_CRAS0] [CENTROID] [RAS2RAS] [NITERSMAX] [FTOL] [LINMINTOL] [SEED] [SAT] [CONF_REF] [NO_BF] [BF_LIM] [BF_NSAMP] [NO_SMOOTH] [REF_FWHM] [MOV_OOB] [INIT_REG_SAVE] [INIT_REG_SAVE_ONLY] [MAT2PAR] [MAT2ROT] [PAR2MAT] [LRREV] [LANDMARKS] [RMS] [MOVOUT] [MOV_IDITHER] [DEBUG] [CHECKOPTS] [VERSION]",
   "container-image": {
     "type": "docker",
     "image": "freesurfer/freesurfer:7.4.1"

diff --git a/descriptors/freesurfer/mri_defacer.json b/descriptors/freesurfer/mri_defacer.json
@@ -3,7 +3,7 @@
   "name": "mri_defacer",
   "author": "FreeSurfer Developers",
   "description": "Tool for defacing MRI images to remove facial features",
-  "command-line": "mri_defacer -[INPUT_VOLUME] -[HEADMASK] -[TEMPSURF] [TEMPLABEL] [WATERMARK] -[DEFACED_VOLUME] [FACEMASK] [FILL_CONSTANTS] [EXCLUDE_MASK] [OPTIONS]",
+  "command-line": "mri_defacer [INPUT_VOLUME] [HEADMASK] [TEMPSURF] [TEMPLABEL] [WATERMARK] [DEFACED_VOLUME] [FACEMASK] [FILL_CONSTANTS] [EXCLUDE_MASK] [TEMPREG] [MINSURFPATH] [MAXSURFPATH] [DISTBOUNDS] [DISTOVERLAY] [DISTDAT] [STATSPATH] [OUTPUT_TEMPSURF] [APPLY_TO_VOLUME] [RIPPLE_CENTER] [APPLY_RIPPLE] [DIAGNOSTIC_LEVEL] [DEBUG] [CHECKOPTS] [VERSION]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_entowm_seg.json b/descriptors/freesurfer/mri_entowm_seg.json
@@ -3,7 +3,7 @@
   "name": "mri_entowm_seg",
   "author": "FreeSurfer Developers",
   "description": "Segment white matter near gyrus ambiens entorhinal cortex using a deep learning model.",
-  "command-line": "mri_entowm_seg [INPUT_IMAGE] [OUTPUT_SEGMENTATION] [RECON_SUBJECTS] [SUBJECTS_DIRECTORY] [OTHER_OPTIONS]",
+  "command-line": "mri_entowm_seg [INPUT_IMAGE] [OUTPUT_SEGMENTATION] [RECON_SUBJECTS] [SUBJECTS_DIRECTORY] [CONFORM] [ETIV] [TAL] [WRITE_POSTERIORS] [WRITE_VOLUMES] [WRITE_QA_STATS] [EXCLUDE_LABELS] [KEEP_AC] [VOX_COUNT_VOLUMES] [MODEL_WEIGHTS] [COLOR_TABLE] [POPULATION_STATS] [DEBUG] [VMP] [THREADS] [SEVEN_TESLA] [PERCENTILE] [CUDA_DEVICE] [OUTPUT_BASE] [NO_CITE_SCLIMBIC] [NCHANNELS]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_evaluate_morph.json b/descriptors/freesurfer/mri_evaluate_morph.json
@@ -2,7 +2,7 @@
   "name": "mri_evaluate_morph",
   "tool-version": "7.4.1",
   "description": "This program computes the overlap of a set of segmentations for a given morph using an xform file.",
-  "command-line": "mri_evaluate_morph [OPTIONS] [XFORM_NAME] [SEGMENTATION_FILES] [OUTPUT_FILE]",
+  "command-line": "mri_evaluate_morph [XFORM_NAME] [SEGMENTATION_FILES] [OUTPUT_FILE]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_fuse_intensity_images.json b/descriptors/freesurfer/mri_fuse_intensity_images.json
@@ -1,7 +1,7 @@
 {
   "name": "mri_fuse_intensity_images",
   "description": "Fuses intensity images based on given transforms",
-  "command-line": "mri_fuse_intensity_images [OPTIONS] [LONGITUDINAL_TIME_POINT_FILE] [INPUT_VOLUME] [TRANSFORM_FILE] [OUTPUT_VOLUME]",
+  "command-line": "mri_fuse_intensity_images [LONGITUDINAL_TIME_POINT_FILE] [INPUT_VOLUME] [TRANSFORM_FILE] [OUTPUT_VOLUME]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_motion_correct.json b/descriptors/freesurfer/mri_motion_correct.json
@@ -3,7 +3,7 @@
   "name": "mri_motion_correct",
   "author": "FreeSurfer Developers",
   "description": "Tool for correcting motion in MRI scans",
-  "command-line": "mri_motion_correct [OUTFILE] [INFILES]...",
+  "command-line": "mri_motion_correct [OUTFILE] [INFILES]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_or.json b/descriptors/freesurfer/mri_or.json
@@ -4,7 +4,7 @@
   "author": "FreeSurfer Developers",
   "descriptor-url": "unknown",
   "description": "Performs a logical voxel-wise OR on a series of volumes",
-  "command-line": "mri_or [OPTIONS] [INPUT_FILES]",
+  "command-line": "mri_or [ORIGINAL_LABELS] [INPUT_FILES]",
   "container-image": {
     "type": "docker",
     "image": "freesurfer/freesurfer:7.4.1"

diff --git a/descriptors/freesurfer/mri_probedicom.json b/descriptors/freesurfer/mri_probedicom.json
@@ -4,7 +4,7 @@
   "author": "FreeSurfer Developers",
   "descriptor-url": "https://surfer.nmr.mgh.harvard.edu/",
   "description": "Utility to probe DICOM files for information.",
-  "command-line": "mri_probedicom [DICOM_FILE] [OPTIONS]",
+  "command-line": "mri_probedicom [DICOM_FILE] [OPTION1] [OPTION2]",
   "container-image": {
     "type": "docker",
     "image": "freesurfer/freesurfer:7.4.1"

diff --git a/descriptors/freesurfer/mri_rf_label.json b/descriptors/freesurfer/mri_rf_label.json
@@ -1,7 +1,7 @@
 {
   "name": "mri_rf_label",
   "description": "MRI automatic tissue labeling using a Gaussian Classifier Atlas (GCA).",
-  "command-line": "mri_ca_label [INPUT_VOLUMES] [TRANSFORM_FILE] [GCAFILE] [OUTPUT_VOLUME] [CROSS_SEQUENCE_FLAG] [NOGIBBS_FLAG] [WM_PATH] [CONFORM_FLAG] [NORMPD_FLAG] [GLA_TL] [DEBUG_VOXEL] [DEBUG_NODE] [DEBUG_LABEL] [TR] [TE] [ALPHA] [EXAMPLE] [PTHRESH] [NITER] [NOVAR_FLAG] [REGULARIZE] [NOHIPPO_FLAG] [FWM] [MRI_VOL] [HEQ] [RENORM] [FLASH_FLAG] [FLASH_PARAMS] [RENORMALIZE] [SET_INPUT] [HISTOGRAM_FLAG] [COND_DENSITY_MEAN] [SNAPSHOTS] [MASK] [EXPAND] [MAX_ITER] [FILTER_MODE] [LONGITUDINAL_VOL] [LONGITUDINAL_LTA] [RELABEL_UNLIKELY_FLAG]",
+  "command-line": "mri_rf_label [INPUT_VOLUMES] [TRANSFORM_FILE] [GCAFILE] [OUTPUT_VOLUME] [CROSS_SEQUENCE_FLAG] [NOGIBBS_FLAG] [WM_PATH] [CONFORM_FLAG] [NORMPD_FLAG] [GCA_TL] [DEBUG_VOXEL] [DEBUG_NODE] [DEBUG_LABEL] [TR] [TE] [ALPHA] [EXAMPLE] [PTHRESH] [NITER] [NOVAR_FLAG] [REGULARIZE] [NOHIPPO_FLAG] [FWM] [MRI_VOL] [HEQ] [RENORM] [FLASH_FLAG] [FLASH_PARAMS] [RENORMALIZE] [SET_INPUT] [HISTOGRAM_FLAG] [COND_DENSITY_MEAN] [SNAPSHOTS] [MASK] [EXPAND] [MAX_ITER] [FILTER_MODE] [LONGITUDINAL_VOL] [LONGITUDINAL_LTA] [RELABEL_UNLIKELY_FLAG]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_rf_train.json b/descriptors/freesurfer/mri_rf_train.json
@@ -3,7 +3,7 @@
   "name": "mri_rf_train",
   "author": "FreeSurfer Developers",
   "description": "Trains GCA data with multiple subjects using MRI data.",
-  "command-line": "mri_rf_train [SEG_VOLUME] [ATLAS_TRANSFORM] [MASK_VOLUME] [NODE_SPACING] [PRIOR_SPACING] [INPUT_TRAINING_DATA...] [SANITY_CHECK] [SUBJECTS] <SUBJECT2> ... [OUTPUT_RFA]",
+  "command-line": "mri_rf_train [SEG_VOLUME] [ATLAS_TRANSFORM] [MASK_VOLUME] [NODE_SPACING] [PRIOR_SPACING] [INPUT_TRAINING_DATA] [SANITY_CHECK] [SUBJECTS] [OUTPUT_RFA]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_robust_register.json b/descriptors/freesurfer/mri_robust_register.json
@@ -3,7 +3,7 @@
   "name": "mri_robust_register",
   "author": "FreeSurfer Developers",
   "description": "Inverse consistent registration of two volumes using robust and standard cost functions.",
-  "command-line": "mri_robust_register -[MOVABLE_VOLUME] -[TARGET_VOLUME] -[OUTPUT_REGISTRATION] [OUTLIER_SENSITIVITY_OPTION] [OPTIONS]",
+  "command-line": "mri_robust_register [MOVABLE_VOLUME] [TARGET_VOLUME] [OUTPUT_REGISTRATION] [OUTLIER_SENSITIVITY] [SATIT] [MAPPED_MOVABLE] [MAPPED_MOVABLE_HDR] [WEIGHTS] [ONEMINUS_W] [ISCALE] [ISCALE_ONLY] [ISCALE_OUT] [ISCALE_IN] [TRANS_ONLY] [AFFINE] [IXFORM] [INIT_ORIENT] [NO_INIT] [VOX2VOX] [COST] [ENT_RADIUS] [ENT_CORRECTION] [ENT_BALL] [ENT_MOV] [POWELL_TOLERANCE] [SOBEL] [NO_SYM] [MAXIMUM_ITERATIONS] [ENT_DST] [HIGH_ITER] [EPS_ITERATION] [NO_MULTISCALE] [MAX_SIZE] [MIN_SIZE] [W_LIMIT] [SUB_SAMPLE] [FLOAT_TYPE] [WHITE_BG_MOV] [WHITE_BG_DST] [UCHAR] [MASK_MOV] [MASK_DST] [HALF_MOV] [HALF_DST] [HALF_WEIGHTS] [HALF_MOV_LTA] [HALF_DST_LTA] [DEBUG] [VERBOSE]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_robust_template.json b/descriptors/freesurfer/mri_robust_template.json
@@ -4,7 +4,7 @@
   "author": "FreeSurfer Developers",
   "descriptor-url": "https://surfer.nmr.mgh.harvard.edu",
   "description": "Constructs an unbiased robust template for longitudinal volumes using an iterative method.",
-  "command-line": "mri_robust_template -[MOV_FILES] -[TEMPLATE_FILE] [SENSITIVITY_OPTION] [LTA_FILES] [MAPMOV_FILES] [MAPMOVHDR_FILES] [WEIGHTS_FILES] [OPTIONS]",
+  "command-line": "mri_robust_template [MOV_FILES] [TEMPLATE_FILE] [SAT_VALUE] [SATIT_FLAG] [LTA_FILES] [MAPMOV_FILES] [MAPMOVHDR_FILES] [WEIGHTS_FILES] [ONEMINUSW_FLAG] [AVERAGE_TYPE] [INITTP] [FIXTP_FLAG] [ISCALE_FLAG] [ISCALEONLY_FLAG] [ISCALEIN_FILES] [ISCALEOUT_FILES] [TRANSONLY_FLAG] [AFFINE_FLAG] [IXFORMS_FILES] [MASKS_FILES] [VOX2VOX_FLAG] [LEASTSQUARES_FLAG] [NOIT_FLAG] [MAXIT] [HIGHIT] [EPSIT] [PAIRMAXIT] [PAIREPSIT] [SUBSAMPLE] [NOMULTI_FLAG] [FLOATTYPE_FLAG] [FINALNEAREST_FLAG] [DOUBLEPREC_FLAG] [CRAS_FLAG] [RES_THRESH] [FROBNORM_THRESH] [DEBUG_FLAG]",
   "container-image": {
     "type": "docker",
     "image": "freesurfer/freesurfer:7.4.1"

diff --git a/descriptors/freesurfer/mri_synthmorph.json b/descriptors/freesurfer/mri_synthmorph.json
@@ -1,7 +1,7 @@
 {
   "name": "mri_synthmorph",
   "tool-version": "7.4.1",
-  "command-line": "mri_synthmorph [MOVING] [FIXED] [MOVED_OUTPUT] [TRANS_OUTPUT] [HEADER_ONLY_FLAG] [MODEL] [INIT_TRANSFORM] [THREADS] [GPU_FLAG] [SMOOTH] [EXTENT] [MODEL_WEIGHTS] [INSPECT_DIR]",
+  "command-line": "mri_synthmorph [MOVING_IMAGE] [FIXED_IMAGE] [MOVED_OUTPUT] [TRANSFORM_OUTPUT] [HEADER_ONLY] [TRANSFORMATION_MODEL] [INIT_TRANSFORM] [THREADS] [GPU_FLAG] [SMOOTH] [EXTENT] [MODEL_WEIGHTS] [INSPECT_DIRECTORY]",
   "description": "SynthMorph is a deep-learning tool for brain-specific MRI image registration without preprocessing.",
   "author": "FreeSurfer Developers",
   "schema-version": "0.5",

diff --git a/descriptors/freesurfer/mri_topologycorrection.json b/descriptors/freesurfer/mri_topologycorrection.json
@@ -1,6 +1,6 @@
 {
   "name": "mri_topologycorrection",
-  "command-line": "mri_topologycorrection [OPTIONS] [INPUT_ORIG_FILE] [INPUT_SEGMENTED_FILE] [OUTPUT_FOLDER]",
+  "command-line": "mri_topologycorrection [INPUT_ORIG_FILE] [INPUT_SEGMENTED_FILE]",
   "schema-version": "0.5",
   "description": "Corrects the topology of segmented MRI images.",
   "inputs": [
@@ -19,15 +19,6 @@
       "optional": false,
       "value-key": "[INPUT_SEGMENTED_FILE]",
       "description": "Path to the segmented image file."
-    },
-    {
-      "id": "options",
-      "name": "Options",
-      "type": "String",
-      "optional": true,
-      "value-key": "[OPTIONS]",
-      "list": true,
-      "description": "Additional options for the mri_topologycorrection command."
     }
   ],
   "output-files": [

diff --git a/descriptors/freesurfer/mri_vol2surf.json b/descriptors/freesurfer/mri_vol2surf.json
@@ -3,7 +3,7 @@
   "name": "mri_vol2surf",
   "author": "FreeSurfer Developers",
   "description": "This program resamples a volume onto a surface of a subject or the sphere. The output can be viewed on the surface (using tksurfer) or can be used for surface-based intersubject averaging.",
-  "command-line": "mri_vol2surf [INPUT_VOLUME] [REGISTRATION_FILE] [OUTPUT_PATH] [OPTIONS]",
+  "command-line": "mri_vol2surf [INPUT_VOLUME] [REGISTRATION_FILE] [OUTPUT_PATH] [REFERENCE_VOLUME] [REGHEADER_SUBJECT] [MNI152REG_FLAG] [TARGET_SUBJECT] [HEMISPHERE] [SURFACE]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mri_voldiff.json b/descriptors/freesurfer/mri_voldiff.json
@@ -3,7 +3,7 @@
   "name": "mri_voldiff",
   "author": "FreeSurfer Developers",
   "description": "Determines whether two volumes are different in terms of pixel data, dimension, precision, resolution, or geometry.",
-  "command-line": "mri_voldiff -[VOLUME1] -[VOLUME2] [VOX2RAS_THRESH] [PIX_THRESH] [ALLOW_PRECISION] [ALLOW_RESOLUTION] [ALLOW_VOX2RAS] [DEBUG] [CHECKOPTS]",
+  "command-line": "mri_voldiff [VOLUME1] [VOLUME2] [VOX2RAS_THRESH] [PIX_THRESH] [ALLOW_PRECISION] [ALLOW_RESOLUTION] [ALLOW_VOX2RAS] [DEBUG] [CHECKOPTS]",
   "schema-version": "0.5",
   "inputs": [
     {

diff --git a/descriptors/freesurfer/mris_compute_acorr.json b/descriptors/freesurfer/mris_compute_acorr.json
@@ -1,7 +1,7 @@
 {
   "name": "mris_compute_acorr",
   "description": "Compute the autocorrelation function of a curvature file on a spherical surface.",
-  "command-line": "mris_compute_acorr [OUTPUT_SUBJECT] [HEMI] [SURF] [CURV] [C1_SUBJECTS] : [C2_SUBJECTS]",
+  "command-line": "mris_compute_acorr [OUTPUT_SUBJECT] [HEMI] [SURF] [CURV] [C1_SUBJECTS] [C2_SUBJECTS]",
   "schema-version": "0.5",
   "inputs": [
     {