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[ENH] outputs corrections #13

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70f3c88
[ENH] outputs corrections
EliseCos Apr 14, 2026
4baf73e
Add singularity option
EliseCos Apr 15, 2026
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2 changes: 1 addition & 1 deletion package-lock.json
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6 changes: 6 additions & 0 deletions src/components/ListOptions.astro
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Expand Up @@ -85,6 +85,12 @@ try {
Apptainer
</label>
</div>
<div style="margin-bottom: 0.5rem;">
<label>
<input type="radio" name="container" value="singularity" />
Singularity
</label>
</div>

<div style="margin-top: 1rem; margin-bottom: 0.5rem;">
<strong>Additional profiles:</strong>
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74 changes: 51 additions & 23 deletions src/content/docs/guides/outputs.mdx
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Expand Up @@ -11,6 +11,13 @@ The directories listed below will be created in the results directory after the
<FileTree>
* result_mouse/
* multiqc/
* stats/
* `all_stats.json`
* `all_stats.xlsx`
* `all_stats_Allen.json`
* `all_stats_Allen.xlsx`
* `all_stats_AllenLR.json`
* `all_stats_AllenLR.xlsx`
* sub-01/
* anat/
* sub-01_masks/
Expand All @@ -19,42 +26,56 @@ The directories listed below will be created in the results directory after the
* `sub-01_atlas-Allen_desc-ANOLR_dseg.nii.gz`
* `sub-01_desc-seeding_mask.nii.gz`
* `sub-01_desc-tracking_mask.nii.gz`
* `sub-01_from-dwi_to-Allen_warp.nii.gz`
* `sub-01_from-Allen_to-dwi_affine.mat`
* `sub-01_from-Allen_to-dwi_warp.nii.gz`
* `sub-01_from-dwi_to-Allen_warp.nii.gz`
* dwi/
* `sub-01_model-csd_param-afd-max_dwimap.nii.gz`
* `sub-01_model-csd_param-afd-sum_dwimap.nii.gz`
* `sub-01_model-csd_param-afd-tot_dwimap.nii.gz`
* `sub-01_model-csd_param-nufo_dwimap.nii.gz`
* `sub-01_model-csd_param-peaks_dwimap.nii.gz`
* `sub-01_model-csd_param-sh_dwimap.nii.gz`
* `sub-01_desc-local_tracking.trk`
* `sub-01_desc-preproc_dwi.nii.gz`
* `sub-01_desc-preproc_dwi.bval`
* `sub-01_desc-preproc_dwi.bvec`
* `sub-01_desc-preproc_dwi.nii.gz`
* `sub-01_label-seeding_desc-local_mask.nii.gz`
* `sub-01_label-tracking_desc-local_mask.nii.gz`
* `sub-01_model-csd_param-afdmax_dwimap.nii.gz`
* `sub-01_model-csd_param-afdsum_dwimap.nii.gz`
* `sub-01_model-csd_param-afdtot_dwimap.nii.gz`
* `sub-01_model-csd_param-peakindices_dwimap.nii.gz`
* `sub-01_model-csd_param-peakindices_dwimap.nii.gz`
* `sub-01_model-csd_param-peakvalues_dwimap.nii.gz`
* `sub-01_model-csd_param-sh_dwimap.nii.gz`
* `sub-01_model-csd_param-nufo_dwimap.nii.gz`
* `sub-01_model-qball_param-apower_dwimap.nii.gz`
* `sub-01_model-qball_param-gfa_dwimap.nii.gz`
* `sub-01_model-qball_param-qball_dwimap.nii.gz`
* `sub-01_model-qball_param-nufo_dwimap.nii.gz`
* `sub-01_model-qball_param-sh_dwimap.nii.gz`
* `sub-01_model-tensor_param-ad_dwimap.nii.gz`
* `sub-01_model-tensor_param-fa_dwimap.nii.gz`
* `sub-01_model-tensor_param-ga_dwimap.nii.gz`
* `sub-01_model-tensor_param-md_dwimap.nii.gz`
* `sub-01_model-tensor_param-mode_dwimap.nii.gz`
* `sub-01_model-tensor_param-rd_dwimap.nii.gz`
* `sub-01_model-tensor_param-residual_dwimap.nii.gz`
* `sub-01_model-tensor_param-rgb_dwimap.nii.gz`
* `sub-01_model-tensor_param-tensor_dwimap.nii.gz`
* `sub-01_model-tensor_param-v1_dwimap.nii.gz`
* `sub-01_model-tensor_param-v2_dwimap.nii.gz`
* `sub-01_model-tensor_param-v3_dwimap.nii.gz`
* `sub-01_mqc.png`
* stats/
* `sub-01_stats.json`
* report/
* `sub-01_multiqc_report.html`
* stats/
* `sub-01_stats.json`
* `sub-01_desc-ANO_stats-mean.csv`
* `sub-01_desc-ANO_stats-std.csv`
* `sub-01_desc-ANOLR_stats-mean.csv`
* `sub-01_desc-ANOLR_stats-std.csv`
* sub-02/
* anat/
* dwi/
* stats/
* report/
* stats/
* ...
* report.html
* work/
</FileTree>

Expand Down Expand Up @@ -82,47 +103,50 @@ In addition to the output files described below, you will also find **sidecar JS
<summary>Output files</summary>

* `dwi/`
* `sub-01_desc-preproc_dwi.nii.gz`: Final preprocessed DWI image in original space.
* `sub-01_desc-preproc_dwi.bval`: Final b-values file.
* `sub-01_desc-preproc_dwi.bvec`: Final corrected b-vectors file.
* `anat/`
* `sub-01_desc-preproc_dwi.nii.gz`: Final preprocessed DWI image in original space.
* `sub-01_desc-preproc_mask.nii.gz`: Final brain mask in original space.
</details>

### **Local Modelling**

<details markdown="1">
<summary>Output files</summary>

* `dwi/`
* `sub-01_model-csd_param-afd-max_dwimap.nii.gz`: Maximum apparent fiber density (AFD) map.
* `sub-01_model-csd_param-afd-sum_dwimap.nii.gz`: Sum of the AFD map.
* `sub-01_model-csd_param-afd-tot_dwimap.nii.gz`: AFD total map.
* `sub-01_model-csd_param-nufo_dwimap.nii.gz`: Number of fiber orientation map.
* `sub-01_model-csd_param-peaks_dwimap.nii.gz`: fODF peaks.
* `sub-01_model-csd_param-afdmax_dwimap.nii.gz`: Maximum apparent fiber density (AFD) map.
* `sub-01_model-csd_param-afdsum_dwimap.nii.gz`: Sum of the AFD map.
* `sub-01_model-csd_param-afdtot_dwimap.nii.gz`: AFD total map.
* `sub-01_model-csd_param-nufo_dwimap.nii.gz`: Number of fiber orientation map based on CSD.
* `sub-01_model-csd_param-peakindices_dwimap.nii.gz`: fODF peaks.
* `sub-01_model-csd_param-peakvalues_dwimap.nii.gz`: fODF peaks.
* `sub-01_model-csd_param-sh_dwimap.nii.gz`: fODF coefficients.
* `sub-01_model-qball_param-apower_dwimap.nii.gz`: Anisotropic power map.
* `sub-01_model-qball_param-gfa_dwimap.nii.gz`: Generalized fractional anisotropy map.
* `sub-01_model-qball_param-nufo_dwimap.nii.gz`: Number of fiber orientation map based on Qball.
* `sub-01_model-qball_param-sh_dwimap.nii.gz`: Spherical harmonics coefficients.
* `sub-01_model-tensor_param-ad_dwimap.nii.gz`: Axial Diffusivity map.
* `sub-01_model-tensor_param-fa_dwimap.nii.gz`: Fractional Anisotropy map.
* `sub-01_model-tensor_param-ga_dwimap.nii.gz`: Geodesic Anisometry map.
* `sub-01_model-tensor_param-md_dwimap.nii.gz`: Mean Diffusivity map.
* `sub-01_model-tensor_param-mode_dwimap.nii.gz`: Mode map.
* `sub-01_model-tensor_param-rd_dwimap.nii.gz`: Radial Diffusivity map.
* `sub-01_model-tensor_param-residual_dwimap.nii.gz`: Residual map of the tensor fit.
* `sub-01_model-tensor_param-rgb_dwimap.nii.gz`: RGB map.
* `sub-01_model-tensor_param-tensor_dwimap.nii.gz`: Tensor map.
* `sub-01_model-tensor_param-v1_dwimap.nii.gz`: Eigenvector 1 of the tensor.
* `sub-01_model-tensor_param-v2_dwimap.nii.gz`: Eigenvector 2 of the tensor.
* `sub-01_model-tensor_param-v3_dwimap.nii.gz`: Eigenvector 3 of the tensor.
</details>

### **Registration**

<details markdown="1">
<summary>Output files</summary>

* `anat/`
* `sub-01_from-dwi_to-Allen_warp.nii.gz`: Non-linear transform from diffusion space to Allen Mouse Brain Atlas space.
* `sub-01_from-Allen_to-dwi_affine.mat`: Affine transform from Allen Mouse Brain Atlas space space to diffusion space.
* `sub-01_from-Allen_to-dwi_warp.nii.gz`: Non-linear transform from Allen Mouse Brain Atlas space to diffusion space.
* `sub-01_from-dwi_to-Allen_warp.nii.gz`: Non-linear transform from diffusion space to Allen Mouse Brain Atlas space.
</details>

### **Segmentation**
Expand Down Expand Up @@ -168,7 +192,11 @@ Within each subject folder, you will find subject-specific HTML reports. Those w
<summary>Output files</summary>

* `stats/`
* `sub-01__stats.json`: Mean and SD for AD, FA, MD and RD for each regions determinated in the nextflow.config
* `sub-01_stats.json`: Mean and SD for AD, FA, MD and RD for each regions determinated in the nextflow.config
* `sub-01_desc-ANO_stats-mean.csv`: Mean for AD, FA, MD and RD for each regions of the Allen Mouse Brain Atlas.
* `sub-01_desc-ANO_stats-std.csv`: SD for AD, FA, MD and RD for each regions of the Allen Mouse Brain Atlas.
* `sub-01_desc-ANOLR_stats-mean.csv`: Mean for AD, FA, MD and RD for each regions of the Allen Mouse Brain Atlas separated left/right.
* `sub-01_desc-ANOLR_stats-std.csv`: SD for AD, FA, MD and RD for each regions of the Allen Mouse Brain Atlas separated left/right.
</details>

### **Pipeline information**
Expand Down