diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2dcb35a..8090e47 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - [2025-01-08]
+
+### `Changed`
+
+- Fastsurfer and freesurfer outputs are now in their own dedicated output folder.
+
 ## [Unreleased] - [2024-12-23]
 
 ### `Added`
diff --git a/conf/modules.config b/conf/modules.config
index 97c9c54..331f68e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -16,30 +16,52 @@ process {
     withName: 'NF_PEDIATRIC:PEDIATRIC:FREESURFERFLOW:FASTSURFER' {
         ext.acq3T = params.acq3T
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/anat/"},
+            [
+                path: { params.fs_output_dir ?: "${params.outdir}/../fastsurfer-v2.3.3/" },
+                mode: params.publish_dir_mode,
+                saveAs: {
+                    filename ->
+                    if ( filename.contains("fastsurfer") ) { "${meta.id}" }
+                    else if ( filename.contains("versions.yml") ) { null }
+                    else { params.lean_output ? null : filename }
+                }
+            ],
+            [
+                path: { "${params.outdir}/${meta.id}/anat/"},
+                mode: params.publish_dir_mode,
+                saveAs: {
+                    filename ->
+                    if ( filename.contains("__final_t1.nii.gz") ) { "${meta.id}_desc-preproc_T1w.nii.gz" }
+                    else if ( filename.contains("versions.yml") ) { null }
+                    else { params.lean_output ? null : filename }
+                }
+            ]
+        ]
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:FREESURFERFLOW:RECONALL' {
+        publishDir = [
+        [
+            path: { params.fs_output_dir ?: "${params.outdir}/../freesurfer-7.4.1/" },
             mode: params.publish_dir_mode,
             saveAs: {
                 filename ->
-                if ( filename.contains("fastsurfer") ) { "${meta.id}_fastsurfer" }
-                else if ( filename.contains("__final_t1.nii.gz") ) { "${meta.id}_desc-preproc_T1w.nii.gz" }
+                if ( filename.contains("recon_all") ) { "${meta.id}" }
                 else if ( filename.contains("versions.yml") ) { null }
                 else { params.lean_output ? null : filename }
             }
-        ]
-    }
-
-    withName: 'NF_PEDIATRIC:PEDIATRIC:FREESURFERFLOW:RECONALL' {
-        publishDir = [
+        ],
+        [
             path: { "${params.outdir}/${meta.id}/anat/" },
             mode: params.publish_dir_mode,
             saveAs: {
                 filename ->
-                if ( filename.contains("recon_all") ) { "${meta.id}_reconall"}
-                else if ( filename.contains("__final_t1.nii.gz") ) { "${meta.id}_desc-preproc_T1w.nii.gz" }
+                if ( filename.contains("__final_t1.nii.gz") ) { "${meta.id}_desc-preproc_T1w.nii.gz" }
                 else if ( filename.contains("versions.yml") ) { null }
                 else { params.lean_output ? null : filename }
             }
         ]
+        ]
     }
 
     withName: 'NF_PEDIATRIC:PEDIATRIC:FREESURFERFLOW:BRAINNETOMECHILD' {
@@ -729,7 +751,7 @@ process {
             mode: params.publish_dir_mode,
             saveAs: {
                 filename ->
-                if ( filename.contains("_warped.nii.gz") ) { "${meta.id}_space-DWI_seg-BrainnetomeChild_dseg.nii.gz" }
+                if ( filename.contains("_warped.nii.gz") ) { "${meta.id}_space-DWI_seg-${params.atlas_name}_dseg.nii.gz" }
                 else if ( filename.contains("versions.yml") ) { null }
                 else { params.lean_output ? null : filename }
             }
diff --git a/docs/output.md b/docs/output.md
index b75a797..21f9f07 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -24,6 +24,20 @@ The directories listed below will be created in the results directory after the
 
 The pipeline will output only the final preprocessed files by default. This behavior is used to limit the number of files generated by the pipeline by omitting the publishing of intermediate files. It is particularly useful when running the pipeline on clusters where file quota are often rapidly met. To opt-out from the lean output version, set the `--lean_output` parameter to false when launching the pipeline (`--lean_output false`).
 
+If you decided to run FreeSurfer or FastSurfer as part of `nf-pediatric`, your output will be located (by default) alongside the `nf-pediatric` output folder. You can select the destination folder by using the `--fs_output_dir` parameter. If you do not specify and output folder destination, it will look like this:
+
+```bash
+<your-nf-pediatric-outdir>
+  |-- multiqc
+  |-- sub-0001
+  |-- sub-0002
+  <...>
+fastsurfer-v2.3.3/
+  |-- sub-0001
+  |-- sub-0002
+  <...>
+```
+
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and data processing steps can be grouped. The final output files are listed below for each of those steps. If you used `--lean_output false`, you will find additional files than the ones described here.
diff --git a/nextflow.config b/nextflow.config
index 28599d8..dd302d2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,6 +17,7 @@ params {
     use_fastsurfer                          = true
     fs_license                              = null
     acq3T                                   = true
+    fs_output_dir                           = null
 
     // Atlas options
     utils_folder                            = "${projectDir}/assets/FS_BN_GL_SF_utils/"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c6b490c..0f666b7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -76,6 +76,14 @@
                     "fa_icon": "fas fa-magnet",
                     "default": true,
                     "hidden": true
+                },
+                "fs_output_dir": {
+                    "type": "string",
+                    "description": "Path to FreeSurfer output directory.",
+                    "fa_icon": "fas fa-folder-open",
+                    "help_text": "Path to FreeSurfer output directory. This is where FreeSurfer will save its output files.",
+                    "format": "directory-path",
+                    "hidden": false
                 }
             }
         },
diff --git a/tests/chained.nf.test b/tests/chained.nf.test
index 6d15029..899de03 100644
--- a/tests/chained.nf.test
+++ b/tests/chained.nf.test
@@ -12,6 +12,7 @@ nextflow_pipeline {
 
                 params.input = "$projectDir/tests/data/samplesheet_testconn.csv"
                 params.outdir = "$outputDir"
+                use_fastsurfer = true
 
                 params.connectomics = true
                 params.freesurfer = true
@@ -23,6 +24,8 @@ nextflow_pipeline {
         then {
             // stable name: All files + folders in ${params.outdir}/ with a stable name.
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore:  ['pipeline_info/*.{html,json,txt}'])
+            // All fastsurfer output.
+            def fastsurfer_output = getAllFilesFromDir("$outputDir/../fastsurfer-v2.3.3/", relative: true, includeDir: true)
             assertAll {
                 assert workflow.success
                 assert snapshot(
@@ -31,7 +34,9 @@ nextflow_pipeline {
                     // Remove the nextflow version from the versions.yml because we test it using different nextflow versions.
                     removeNextflowVersion("$outputDir/pipeline_info/pipeline_software_mqc_versions.yml"),
                     // All stable name.
-                    stable_name
+                    stable_name,
+                    // All fastsurfer output.
+                    fastsurfer_output
                 ).match()
             }
         }
@@ -88,6 +93,8 @@ nextflow_pipeline {
         then {
             // stable name: All files + folders in ${params.outdir}/ with a stable name.
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore:  ['pipeline_info/*.{html,json,txt}'])
+            // All fastsurfer output.
+            def fastsurfer_output = getAllFilesFromDir("$outputDir/../fastsurfer-v2.3.3/", relative: true, includeDir: true)
             assertAll {
                 assert workflow.success
                 assert snapshot(
@@ -96,7 +103,9 @@ nextflow_pipeline {
                     // Remove the nextflow version from the versions.yml because we test it using different nextflow versions.
                     removeNextflowVersion("$outputDir/pipeline_info/pipeline_software_mqc_versions.yml"),
                     // All stable name.
-                    stable_name
+                    stable_name,
+                    // All fastsurfer output.
+                    fastsurfer_output
                 ).match()
             }
         }
diff --git a/tests/chained.nf.test.snap b/tests/chained.nf.test.snap
index 0f9caca..d0bf453 100644
--- a/tests/chained.nf.test.snap
+++ b/tests/chained.nf.test.snap
@@ -351,7 +351,6 @@
                 "sub-test",
                 "sub-test/anat",
                 "sub-test/anat/sub-test_desc-preproc_T1w.nii.gz",
-                "sub-test/anat/sub-test_fastsurfer",
                 "sub-test/anat/sub-test_from-T1w_to-dwi_affine.mat",
                 "sub-test/anat/sub-test_from-T1w_to-dwi_warp.nii.gz",
                 "sub-test/anat/sub-test_from-dwi_to-T1w_warp.nii.gz",
@@ -429,13 +428,17 @@
                 "sub-test/multiqc/sub-test_multiqc_plots",
                 "sub-test/multiqc/sub-test_multiqc_report.html",
                 "subcortical_volumes.tsv"
+            ],
+            [
+                "",
+                "sub-test"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2025-01-03T09:26:58.519601"
+        "timestamp": "2025-01-08T10:10:09.573439"
     },
     "Freesurfer + connectomics profiles - should run successfully": {
         "content": [
@@ -482,7 +485,6 @@
                 "sub-test",
                 "sub-test/anat",
                 "sub-test/anat/sub-test_desc-preproc_T1w.nii.gz",
-                "sub-test/anat/sub-test_fastsurfer",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_desc-labels.json",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_desc-labels.txt",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_dseg.nii.gz",
@@ -512,13 +514,17 @@
                 "sub-test/multiqc/sub-test_multiqc_plots",
                 "sub-test/multiqc/sub-test_multiqc_report.html",
                 "subcortical_volumes.tsv"
+            ],
+            [
+                "",
+                "sub-test"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2025-01-03T09:22:33.330752"
+        "timestamp": "2025-01-08T10:05:54.243678"
     },
     "Connectomics + tracking profiles - should run successfully": {
         "content": [
diff --git a/tests/freesurfer.nf.test b/tests/freesurfer.nf.test
index 83b2f96..493a0e0 100644
--- a/tests/freesurfer.nf.test
+++ b/tests/freesurfer.nf.test
@@ -13,6 +13,7 @@ nextflow_pipeline {
                 input = "$projectDir/tests/data/samplesheet_testtracking.csv"
                 outdir = "$outputDir"
 
+                use_fastsurfer = false
                 freesurfer = true
                 fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
 
@@ -22,6 +23,8 @@ nextflow_pipeline {
         then {
             // stable name: All files + folders in ${params.outdir}/ with a stable name.
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore:  ['pipeline_info/*.{html,json,txt}'])
+            // All freesurfer output.
+            def freesurfer_output = getAllFilesFromDir("$outputDir/../freesurfer-7.4.1/", relative: true, includeDir: true)
             assertAll {
                 assert workflow.success
                 assert snapshot(
@@ -30,7 +33,9 @@ nextflow_pipeline {
                     // Remove the nextflow version from the versions.yml because we test it using different nextflow versions.
                     removeNextflowVersion("$outputDir/pipeline_info/pipeline_software_mqc_versions.yml"),
                     // All stable name.
-                    stable_name
+                    stable_name,
+                    // All freesurfer output.
+                    freesurfer_output
                 ).match()
             }
         }
@@ -43,6 +48,7 @@ nextflow_pipeline {
 
                 params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
                 params.outdir = "$outputDir"
+                params.fs_output_dir = "$outputDir/../onedirdown/fastsurfer-v2.3.3"
 
                 params.freesurfer = true
                 params.use_fastsurfer = true
@@ -54,6 +60,8 @@ nextflow_pipeline {
         then {
             // stable name: All files + folders in ${params.outdir}/ with a stable name.
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore:  ['pipeline_info/*.{html,json,txt}'])
+            // All fastsurfer output.
+            def fastsurfer_output = getAllFilesFromDir(params.fs_output_dir, relative: true, includeDir: true)
             assertAll {
                 assert workflow.success
                 assert snapshot(
@@ -62,7 +70,9 @@ nextflow_pipeline {
                     // Remove the nextflow version from the versions.yml because we test it using different nextflow versions.
                     removeNextflowVersion("$outputDir/pipeline_info/pipeline_software_mqc_versions.yml"),
                     // All stable name.
-                    stable_name
+                    stable_name,
+                    // All fastsurfer output.
+                    fastsurfer_output
                 ).match()
             }
         }
diff --git a/tests/freesurfer.nf.test.snap b/tests/freesurfer.nf.test.snap
index 891364c..a16d5dd 100644
--- a/tests/freesurfer.nf.test.snap
+++ b/tests/freesurfer.nf.test.snap
@@ -26,7 +26,6 @@
                 "sub-test",
                 "sub-test/anat",
                 "sub-test/anat/sub-test_desc-preproc_T1w.nii.gz",
-                "sub-test/anat/sub-test_fastsurfer",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_desc-labels.json",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_desc-labels.txt",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_dseg.nii.gz",
@@ -45,20 +44,24 @@
                 "sub-test/multiqc/sub-test_multiqc_plots",
                 "sub-test/multiqc/sub-test_multiqc_report.html",
                 "subcortical_volumes.tsv"
+            ],
+            [
+                "",
+                "sub-test"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2025-01-02T23:01:18.627052"
+        "timestamp": "2025-01-08T09:57:43.80135"
     },
     "Freesurfer profile - freesurfer - should run successfully": {
         "content": [
             6,
             {
-                "FASTSURFER": {
-                    "fastsurfer": "2.3.3+0000000"
+                "RECONALL": {
+                    "freesurfer": "7.4.1"
                 },
                 "Workflow": {
                     "nf/pediatric": "v1.0dev"
@@ -80,7 +83,6 @@
                 "sub-test",
                 "sub-test/anat",
                 "sub-test/anat/sub-test_desc-preproc_T1w.nii.gz",
-                "sub-test/anat/sub-test_fastsurfer",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_desc-labels.json",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_desc-labels.txt",
                 "sub-test/anat/sub-test_seg-BrainnetomeChild_dseg.nii.gz",
@@ -99,12 +101,16 @@
                 "sub-test/multiqc/sub-test_multiqc_plots",
                 "sub-test/multiqc/sub-test_multiqc_report.html",
                 "subcortical_volumes.tsv"
+            ],
+            [
+                "",
+                "sub-test"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2025-01-02T22:41:26.12873"
+        "timestamp": "2025-01-08T10:01:23.448734"
     }
 }
\ No newline at end of file
diff --git a/tests/multisubjects.nf.test b/tests/multisubjects.nf.test
index ab49399..8ba466d 100644
--- a/tests/multisubjects.nf.test
+++ b/tests/multisubjects.nf.test
@@ -12,6 +12,7 @@ nextflow_pipeline {
 
                 params.input = "$projectDir/tests/data/samplesheet_multisubject.csv"
                 params.outdir = "$outputDir"
+                params.use_fastsurfer = true
 
                 params.connectomics = true
                 params.tracking = true
@@ -24,6 +25,8 @@ nextflow_pipeline {
         then {
             // stable name: All files + folders in ${params.outdir}/ with a stable name.
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore:  ['pipeline_info/*.{html,json,txt}'])
+            // All fastsurfer output.
+            def fastsurfer_output = getAllFilesFromDir("$outputDir/../fastsurfer-v2.3.3/", relative: true, includeDir: true)
             assertAll {
                 assert workflow.success
                 assert snapshot(
@@ -32,7 +35,9 @@ nextflow_pipeline {
                     // Remove the nextflow version from the versions.yml because we test it using different nextflow versions.
                     removeNextflowVersion("$outputDir/pipeline_info/pipeline_software_mqc_versions.yml"),
                     // All stable name.
-                    stable_name
+                    stable_name,
+                    // All fastsurfer output.
+                    fastsurfer_output
                 ).match()
             }
         }
diff --git a/tests/multisubjects.nf.test.snap b/tests/multisubjects.nf.test.snap
index 1b030e7..6be5c56 100644
--- a/tests/multisubjects.nf.test.snap
+++ b/tests/multisubjects.nf.test.snap
@@ -273,7 +273,6 @@
                 "sub-test1",
                 "sub-test1/anat",
                 "sub-test1/anat/sub-test1_desc-preproc_T1w.nii.gz",
-                "sub-test1/anat/sub-test1_fastsurfer",
                 "sub-test1/anat/sub-test1_from-T1w_to-dwi_affine.mat",
                 "sub-test1/anat/sub-test1_from-T1w_to-dwi_warp.nii.gz",
                 "sub-test1/anat/sub-test1_from-dwi_to-T1w_warp.nii.gz",
@@ -353,7 +352,6 @@
                 "sub-test2",
                 "sub-test2/anat",
                 "sub-test2/anat/sub-test2_desc-preproc_T1w.nii.gz",
-                "sub-test2/anat/sub-test2_fastsurfer",
                 "sub-test2/anat/sub-test2_from-T1w_to-dwi_affine.mat",
                 "sub-test2/anat/sub-test2_from-T1w_to-dwi_warp.nii.gz",
                 "sub-test2/anat/sub-test2_from-dwi_to-T1w_warp.nii.gz",
@@ -431,12 +429,17 @@
                 "sub-test2/multiqc/sub-test2_multiqc_plots",
                 "sub-test2/multiqc/sub-test2_multiqc_report.html",
                 "subcortical_volumes.tsv"
+            ],
+            [
+                "",
+                "sub-test1",
+                "sub-test2"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2025-01-03T09:38:36.893058"
+        "timestamp": "2025-01-08T13:42:46.737348"
     }
 }
\ No newline at end of file