Various fixes to descriptors used for distortion correction

src/niwrap/fsl/6.0.4/applytopup/boutiques.json

@@ -116,7 +116,7 @@
   "schema-version": "0.5+styx",
   "output-files": [
     {
-      "path-template": "[OUT]",
+      "path-template": "[OUT].nii.gz",
       "description": "The output warped image.",
       "id": "output_file",
       "name": "Warped image"

src/niwrap/fsl/6.0.4/convertwarp/boutiques.json

@@ -1,6 +1,6 @@
 {
   "name": "convertwarp",
-  "command-line": "convertwarp [ABSWARP] [CONS_JACOBIAN] [JACOBIAN_MAX] [JACOBIAN_MIN] [MIDMAT] [OUT_ABSWARP] [OUT_RELWARP] [OUTPUT_TYPE] [POSTMAT] [PREMAT] [REFERENCE] [RELWARP] [SHIFT_DIRECTION] [SHIFT_IN_FILE] [WARP1] [WARP2]",
+  "command-line": "convertwarp [ABSWARP] [CONS_JACOBIAN] [JACOBIAN_MAX] [JACOBIAN_MIN] [MIDMAT] [OUT] [OUT_ABSWARP] [OUT_RELWARP] [OUTPUT_TYPE] [POSTMAT] [PREMAT] [REFERENCE] [RELWARP] [SHIFT_DIRECTION] [SHIFT_IN_FILE] [WARP1] [WARP2]",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Use FSL convertwarp for combining multiple transforms into one.",
   "url": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki",
@@ -51,6 +51,16 @@
       "description": "Name of file containing mid-warp-affine transform.",
       "optional": true
     },
+    {
+      "id": "out",
+      "name": "Out",
+      "type": "String",
+      "value-key": "[OUT]",
+      "command-line-flag": "--out",
+      "command-line-flag-separator": "=",
+      "description": "Name of output file, containing warps that are the combination of all those given as arguments. the format of this will be a field-file (rather than spline coefficients) with any affine components included.",
+      "optional": false
+    },
     {
       "id": "out_abswarp",
       "name": "Out abswarp",
@@ -173,13 +183,7 @@
       "name": "Out file",
       "id": "out_file",
       "description": "Name of output file, containing warps that are the combination of all those given as arguments. the format of this will be a field-file (rather than spline coefficients) with any affine components included.",
-      "path-template": "[REFERENCE]_concatwarp"
-    },
-    {
-      "name": "Out file",
-      "id": "out_file",
-      "path-template": "out_file",
-      "description": "Name of output file, containing the warp as field or coefficients."
+      "path-template": "[OUT]"
     }
   ],
   "schema-version": "0.5+styx"

src/niwrap/fsl/6.0.4/fslmerge/boutiques.json

@@ -91,7 +91,7 @@
   "schema-version": "0.5+styx",
   "output-files": [
     {
-      "path-template": "[OUTPUT_FILE]",
+      "path-template": "[OUTPUT_FILE].nii.gz",
       "description": "Output concatenated image file",
       "id": "out_file",
       "name": "Output File"

src/niwrap/fsl/6.0.4/fugue/boutiques.json

@@ -1,6 +1,6 @@
 {
   "name": "fugue",
-  "command-line": "fugue [ASYM_SE_TIME] [DESPIKE_2DFILTER] [DESPIKE_THRESHOLD] [DWELL_TIME] [DWELL_TO_ASYM_RATIO] [FMAP_IN_FILE] [FMAP_OUT_FILE] [FORWARD_WARPING] [FOURIER_ORDER] [ICORR] [ICORR_ONLY] [IN_FILE] [MASK_FILE] [MEDIAN_2DFILTER] [NO_EXTEND] [NO_GAP_FILL] [NOKSPACE] [OUTPUT_TYPE] [PAVA] [PHASE_CONJUGATE] [PHASEMAP_IN_FILE] [POLY_ORDER] [SAVE_FMAP] [SAVE_SHIFT] [SAVE_UNMASKED_FMAP] [SAVE_UNMASKED_SHIFT] [SHIFT_IN_FILE] [SHIFT_OUT_FILE] [SMOOTH2D] [SMOOTH3D] [UNWARP_DIRECTION] [UNWARPED_FILE] [WARPED_FILE]",
+  "command-line": "fugue [ASYM_SE_TIME] [DESPIKE_2DFILTER] [DESPIKE_THRESHOLD] [DWELL_TIME] [DWELL_TO_ASYM_RATIO] [FMAP_IN_FILE] [FMAP_OUT_FILE] [FORWARD_WARPING] [FOURIER_ORDER] [ICORR] [ICORR_ONLY] [IN_FILE] [MASK_FILE] [MEDIAN_2DFILTER] [NO_EXTEND] [NO_GAP_FILL] [NOKSPACE] [OUTPUT_TYPE] [PAVA] [PHASE_CONJUGATE] [PHASEMAP_IN_FILE] [POLY_ORDER] [SAVE_UNMASKED_FMAP] [SAVE_UNMASKED_SHIFT] [SHIFT_IN_FILE] [SHIFT_OUT_FILE] [SMOOTH2D] [SMOOTH3D] [UNWARP_DIRECTION] [UNWARPED_FILE] [WARPED_FILE]",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "FMRIB's Utility for Geometric Unwarping of EPIs",
   "url": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki",
@@ -212,22 +212,6 @@
       "description": "Apply polynomial fitting of order n.",
       "optional": true
     },
-    {
-      "id": "save_fmap",
-      "name": "Save fmap",
-      "type": "Flag",
-      "value-key": "[SAVE_FMAP]",
-      "command-line-flag": "--save_fmap",
-      "description": "Write field map volume."
-    },
-    {
-      "id": "save_shift",
-      "name": "Save shift",
-      "type": "Flag",
-      "value-key": "[SAVE_SHIFT]",
-      "command-line-flag": "--save_shift",
-      "description": "Write pixel shift volume."
-    },
     {
       "id": "save_unmasked_fmap",
       "name": "Save unmasked fmap",

src/niwrap/fsl/6.0.4/topup/boutiques.json

@@ -262,13 +262,13 @@
       "name": "Movement parameters file"
     },
     {
-      "path-template": "[FOUT]",
+      "path-template": "[FOUT].nii.gz",
       "description": "Image file with field (Hz)",
       "id": "fout",
       "name": "Field image"
     },
     {
-      "path-template": "[IOUT]",
+      "path-template": "[IOUT].nii.gz",
       "description": "4D image file with unwarped images",
       "id": "iout",
       "name": "Unwarped images"