Update FSL for new container

README.md

@@ -1,9 +1,7 @@
-
 # NiWrap <img src="logo.png" align="right" width="25%"/>
 
 🧠 Modern Python wrappers for neuroimaging tools
 
-
 ## 🚀 Features
 
 - Extensive collection of neuroimaging command line tool metadata
@@ -15,22 +13,23 @@
 
 <!-- START_PACKAGES_TABLE -->
 
-| Package | Status | Version | API Coverage |
-| --- | --- | --- | --- |
-| [AFNI](https://afni.nimh.nih.gov/) | In progress | [`24.2.06`](https://hub.docker.com/r/afni/afni_make_build) | 532/658 (80.9%) |
-| [ANTs](https://github.com/ANTsX/ANTs) | In progress | [`2.5.3`](https://hub.docker.com/r/antsx/ants) | 71/113 (62.8%) |
-| [Connectome Workbench](https://github.com/Washington-University/workbench) | Testing | [`1.5.0`](https://hub.docker.com/r/brainlife/connectome_workbench) | 202/202 (100% 🎉) |
-| [Convert3D](http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D) | In progress | [`1.1.0`](https://hub.docker.com/r/pyushkevich/itksnap) | 2/4 (50.0%) |
-| [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) | In progress | [`6.0.5`](https://hub.docker.com/r/brainlife/fsl) | 254/338 (75.1%) |
-| [FreeSurfer](https://github.com/freesurfer/freesurfer) | In progress | [`7.4.1`](https://hub.docker.com/r/freesurfer/freesurfer) | 713/806 (88.5%) |
-| [Greedy](https://sites.google.com/view/greedyreg/about) | In progress | [`1.0.1`](https://hub.docker.com/r/pyushkevich/itksnap) | 1/1 (100% 🎉) |
-| [MRTrix3](https://www.mrtrix.org/) | Testing | [`3.0.4`](https://hub.docker.com/r/mrtrix3/mrtrix3) | 117/125 (93.6%) |
-| [MRTrix3Tissue](https://3tissue.github.io/) | Testing | [`5.2.8`](https://hub.docker.com/r/brainlife/3tissue) | 1/1 (100% 🎉) |
-| [NiftyReg](http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg) | In progress | [`1.4.0`](https://hub.docker.com/r/vnmd/niftyreg_1.4.0) | 7/7 (100% 🎉) |
+| Package                                                                     | Status      | Version                                                            | API Coverage      |
+| --------------------------------------------------------------------------- | ----------- | ------------------------------------------------------------------ | ----------------- |
+| [AFNI](https://afni.nimh.nih.gov/)                                          | In progress | [`24.2.06`](https://hub.docker.com/r/afni/afni_make_build)         | 532/658 (80.9%)   |
+| [ANTs](https://github.com/ANTsX/ANTs)                                       | In progress | [`2.5.3`](https://hub.docker.com/r/antsx/ants)                     | 71/113 (62.8%)    |
+| [Connectome Workbench](https://github.com/Washington-University/workbench)  | Testing     | [`1.5.0`](https://hub.docker.com/r/brainlife/connectome_workbench) | 202/202 (100% 🎉) |
+| [Convert3D](http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D) | In progress | [`1.1.0`](https://hub.docker.com/r/pyushkevich/itksnap)            | 2/4 (50.0%)       |
+| [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)                               | In progress | [`6.0.4`](https://hub.docker.com/r/brainlife/fsl)                  | 241/312 (77.2%)   |
+| [FreeSurfer](https://github.com/freesurfer/freesurfer)                      | In progress | [`7.4.1`](https://hub.docker.com/r/freesurfer/freesurfer)          | 713/806 (88.5%)   |
+| [Greedy](https://sites.google.com/view/greedyreg/about)                     | In progress | [`1.0.1`](https://hub.docker.com/r/pyushkevich/itksnap)            | 1/1 (100% 🎉)     |
+| [MRTrix3](https://www.mrtrix.org/)                                          | Testing     | [`3.0.4`](https://hub.docker.com/r/mrtrix3/mrtrix3)                | 117/125 (93.6%)   |
+| [MRTrix3Tissue](https://3tissue.github.io/)                                 | Testing     | [`5.2.8`](https://hub.docker.com/r/brainlife/3tissue)              | 1/1 (100% 🎉)     |
+| [NiftyReg](http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg)             | In progress | [`1.4.0`](https://hub.docker.com/r/vnmd/niftyreg_1.4.0)            | 7/7 (100% 🎉)     |
 
 <!-- END_PACKAGES_TABLE -->
 
 > 📊 **API Coverage Explained**
+>
 > - Represents the percentage of tool binaries with available NiWrap descriptors
 > - Does not indicate descriptor completeness
 > - 100% coverage isn't always necessary (e.g., some FSL/AFNI utilities have Python stdlib equivalents)
@@ -63,7 +62,6 @@ See the [NiWrap Python package readme](https://github.com/childmindresearch/niwr
 
 Contributions are welcome! See [CONTRIBUTING.md](./CONTRIBUTING.md) for ways to get started.
 
-
 ## 📄 License
 
 The NiWrap project itself, including all metadata and generated Python wrappers, is licensed under the MIT License. See the LICENSE file for details.

descriptors/fsl/AnatomicalAverage.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "AnatomicalAverage",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "https://example.com/anatomicalaverage.json",

descriptors/fsl/aff2rigid.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "aff2rigid",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Tool for converting affine transformations to rigid transformations.",

descriptors/fsl/applytopup.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "applytopup",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "applytopup applies corrections to images using the field estimates produced by topup.",

descriptors/fsl/applywarp.json

@@ -178,7 +178,7 @@
       "mutually-exclusive": true
     }
   ],
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "schema-version": "0.5",
   "container-image": {
     "type": "docker",

descriptors/fsl/applyxfm4D.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "applyxfm4D",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Applies 4D transformation matrices to 4D volumes",

descriptors/fsl/asl_file.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "asl_file",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "ASL data manipulation tool for FSL",

descriptors/fsl/asl_mfree.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "asl_mfree",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "ASL model-free analysis tool",

descriptors/fsl/atlasquery.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "atlasquery",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Structural lookup tool for FSL atlases.",

descriptors/fsl/avscale.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "avscale",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "A command line tool for computing affine transformations.",

descriptors/fsl/avw2fsl.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "avw2fsl",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "https://example.com/avw2fsl.json",

descriptors/fsl/b0calc.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "b0calc",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "B0 field calculation program",

descriptors/fsl/basil_var.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "basil_var",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Variance calculator for BASIL",

descriptors/fsl/baycest.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "baycest",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Bayesian analysis for chemical exchange saturation transfer z-spectra",

descriptors/fsl/bedpostx.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bedpostx",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX",

descriptors/fsl/bedpostx_datacheck.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bedpostx_datacheck",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Check the data directory for BEDPOSTX compatibility",

descriptors/fsl/bedpostx_gpu.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bedpostx_gpu",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Probabilistic tractography and diffusion MRI fitting tool",

descriptors/fsl/bet.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bet",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "https://github.com/aces/cbrain-plugins-neuro/blob/master/cbrain_task_descriptors/fsl_bet.json",

descriptors/fsl/bet2.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bet2",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Automated brain extraction tool for FSL",

descriptors/fsl/betsurf.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "betsurf",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "BET Surface Finder to extract brain surfaces using T1 and T2 images",

descriptors/fsl/bianca.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bianca",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "BIANCA: Brain Intensity AbNormality Classification Algorithm",

descriptors/fsl/bianca_cluster_stats.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bianca_cluster_stats",
   "description": "Calculate number of clusters and WMH volume in a BIANCA output map",
   "command-line": "bianca_cluster_stats [BIANCA_OUTPUT_MAP] [THRESHOLD] [MIN_CLUSTER_SIZE] [MASK]",

descriptors/fsl/bianca_overlap_measures.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "bianca_overlap_measures",
   "description": "BIANCA overlap measures script for FSL",
   "author": "FMRIB Analysis Group, University of Oxford",

descriptors/fsl/calc_grad_perc_dev.json

@@ -1,6 +1,6 @@
 {
   "name": "calc_grad_perc_dev",
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "http://example.com/descriptor-url",
   "description": "Compute the gradient percent deviation based on a full warp image from gradient_unwarp.py",

descriptors/fsl/ccops.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "ccops",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/",

descriptors/fsl/checkFEAT.json

@@ -21,7 +21,7 @@
     }
   ],
   "schema-version": "0.5",
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "http://example.com/checkFEAT_descriptor.json",
   "url": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki",

descriptors/fsl/fsl-cluster.json → descriptors/fsl/cluster.json

@@ -1,6 +1,6 @@
 {
-  "name": "fsl-cluster",
-  "command-line": "fsl-cluster [CONNECTIVITY] [COPE_FILE] [DLH] [FIND_MIN] [FRACTIONAL] [IN_FILE] [MINCLUSTERSIZE] [NO_TABLE] [NUM_MAXIMA] [OUT_INDEX_FILE] [OUT_LOCALMAX_TXT_FILE] [OUT_LOCALMAX_VOL_FILE] [OUT_MAX_FILE] [OUT_MEAN_FILE] [OUT_PVAL_FILE] [OUT_SIZE_FILE] [OUT_THRESHOLD_FILE] [OUTPUT_TYPE] [PEAK_DISTANCE] [PTHRESHOLD] [STD_SPACE_FILE] [THRESHOLD] [USE_MM] [VOLUME] [WARPFIELD_FILE] [XFM_FILE]",
+  "name": "cluster",
+  "command-line": "cluster [CONNECTIVITY] [COPE_FILE] [DLH] [FIND_MIN] [FRACTIONAL] [IN_FILE] [MINCLUSTERSIZE] [NO_TABLE] [NUM_MAXIMA] [OUT_INDEX_FILE] [OUT_LOCALMAX_TXT_FILE] [OUT_LOCALMAX_VOL_FILE] [OUT_MAX_FILE] [OUT_MEAN_FILE] [OUT_PVAL_FILE] [OUT_SIZE_FILE] [OUT_THRESHOLD_FILE] [OUTPUT_TYPE] [PEAK_DISTANCE] [PTHRESHOLD] [STD_SPACE_FILE] [THRESHOLD] [USE_MM] [VOLUME] [WARPFIELD_FILE] [XFM_FILE]",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Uses FSL cluster to perform clustering on statistical output",
   "inputs": [
@@ -456,7 +456,7 @@
       "mutually-exclusive": true
     }
   ],
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "schema-version": "0.5",
   "container-image": {
     "type": "docker",

descriptors/fsl/cluster2html.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "cluster2html",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Generates an HTML report from cluster-based FEAT analysis",

descriptors/fsl/concat_bvars.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "concat_bvars",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Concatenate multiple .bvars files into a single .bvars file",

descriptors/fsl/connectedcomp.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "connectedcomp",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Connected component analysis tool",

descriptors/fsl/convert_xfm.json

@@ -67,7 +67,7 @@
       "mutually-exclusive": true
     }
   ],
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "schema-version": "0.5",
   "container-image": {
     "type": "docker",

descriptors/fsl/convertwarp.json

@@ -195,7 +195,7 @@
       "mutually-exclusive": true
     }
   ],
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "schema-version": "0.5",
   "container-image": {
     "type": "docker",

descriptors/fsl/create_lut.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "create_lut",
   "description": "A tool to create lookup tables",
   "command-line": "create_lut [OUTPUT_FILE_ROOT]",

descriptors/fsl/cutoffcalc.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "cutoffcalc",
   "author": "FMRIB Analysis Group, University of Oxford",
   "descriptor-url": "https://github.com/aces/cbrain-plugins-neuro/blob/master/descriptors/fsl_cutoffcalc.json",

descriptors/fsl/design_ttest2.json

@@ -1,5 +1,5 @@
 {
-  "tool-version": "6.0.5",
+  "tool-version": "6.0.4",
   "name": "design_ttest2",
   "author": "FMRIB Analysis Group, University of Oxford",
   "description": "Command for generating group mean contrasts for a two-sample t-test design.",