From dda075760b8a346a291e4246d59d9d54c0289075 Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Mon, 6 Jan 2025 09:10:03 -0600
Subject: [PATCH 01/10] Create fmriprep-DARBY-PDK_v24.1.1.yaml

---
 fmriprep-DARBY-PDK_v24.1.1.yaml | 90 +++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100644 fmriprep-DARBY-PDK_v24.1.1.yaml

diff --git a/fmriprep-DARBY-PDK_v24.1.1.yaml b/fmriprep-DARBY-PDK_v24.1.1.yaml
new file mode 100644
index 0000000..c544bb4
--- /dev/null
+++ b/fmriprep-DARBY-PDK_v24.1.1.yaml
@@ -0,0 +1,90 @@
+---
+procyamlversion: 3.0.0-dev.0
+
+description: fmriprep - https://fmriprep.org/en/stable/
+
+jobtemplate: job_template_v3.txt
+
+containers:
+  - name: fmriprep
+    path: fmriprep_24.1.1.sif
+    source: docker://nipreps/fmriprep:24.1.1
+
+requirements:
+  walltime: 2-0
+  memory: 24000
+
+inputs:
+  xnat:
+
+    scans:
+
+      - name: scan_t1
+        types: 'Sagittal 3D Accelerated MPRAGE'
+        keep_multis: first
+        resources:
+          - {resource: NIFTI, fmatch: '*.nii.gz', fdest: t1.nii.gz}
+          - {resource: JSON, fmatch: '*.json', fdest: t1.json}
+
+      - name: scan_fmri
+        types: 'Axial fcMRI (EYES OPEN)'
+        resources:
+          - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz}
+          - {resource: JSON, fmatch: '*.json', fdest: fmri.json}
+
+    assessors:
+        - name: assr_fs
+          proctypes: freesurfer720_v2
+          resources:
+            - {resource: SUBJECT, ftype: DIR, fdest: SUBJECT}
+
+    attrs:
+      - {varname: subject, object: session, attr: subject_label}
+      - {varname: session, object: session, attr: label}
+
+outputs:
+  - {path: sourcedata, type: DIR, resource: sourcedata}
+  - {path: HTML, type: DIR, resource: HTML}
+  - {path: BIDS, type: DIR, resource: fmriprepBIDS}
+
+pre:
+  type: singularity_exec
+  container: fmriprep
+  args: >-
+    bash -c '
+    cd /INPUTS &&
+    curl -o v1.5.1.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.5.1.tar.gz &&
+    tar -zxf v1.5.1.tar.gz &&
+    export PATH=/INPUTS/fmriprep-prep-1.5.1/src:\$PATH &&
+    fmriprep-prep.sh
+      --t1_niigz /INPUTS/t1.nii.gz
+      --bids_dir /INPUTS/BIDS
+      --sub {subject}
+      --ses {session}
+      --fmri_niigzs /INPUTS/fmri.nii.gz 
+      --slicetiming Philips_DEFAULT_k
+    '
+
+command:
+  type: singularity_run
+  container: fmriprep
+  args: >-
+    --notrack
+    --output-spaces MNI152NLin2009cAsym
+    --ignore slicetiming
+    --fs-license-file /opt/license.txt
+    /INPUTS/BIDS
+    /OUTPUTS/BIDS
+    participant
+  extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt
+
+post:
+  type: singularity_exec
+  container: fmriprep
+  args: >-
+    bash -c '
+    mkdir /OUTPUTS/HTML &&
+    cp /OUTPUTS/BIDS/sub-*.html /OUTPUTS/HTML &&
+    cp -R /OUTPUTS/BIDS/sub-*/figures /OUTPUTS/HTML/sub-* &&
+    mv /OUTPUTS/BIDS/sourcedata /OUTPUTS/sourcedata
+    '

From 29243912aa5eb0147c6d07a59e0831b679b1f3dc Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Mon, 27 Jan 2025 09:22:47 -0600
Subject: [PATCH 02/10] Delete fmriprep-DARBY-PDK_v24.1.1.yaml

---
 fmriprep-DARBY-PDK_v24.1.1.yaml | 90 ---------------------------------
 1 file changed, 90 deletions(-)
 delete mode 100644 fmriprep-DARBY-PDK_v24.1.1.yaml

diff --git a/fmriprep-DARBY-PDK_v24.1.1.yaml b/fmriprep-DARBY-PDK_v24.1.1.yaml
deleted file mode 100644
index c544bb4..0000000
--- a/fmriprep-DARBY-PDK_v24.1.1.yaml
+++ /dev/null
@@ -1,90 +0,0 @@
----
-procyamlversion: 3.0.0-dev.0
-
-description: fmriprep - https://fmriprep.org/en/stable/
-
-jobtemplate: job_template_v3.txt
-
-containers:
-  - name: fmriprep
-    path: fmriprep_24.1.1.sif
-    source: docker://nipreps/fmriprep:24.1.1
-
-requirements:
-  walltime: 2-0
-  memory: 24000
-
-inputs:
-  xnat:
-
-    scans:
-
-      - name: scan_t1
-        types: 'Sagittal 3D Accelerated MPRAGE'
-        keep_multis: first
-        resources:
-          - {resource: NIFTI, fmatch: '*.nii.gz', fdest: t1.nii.gz}
-          - {resource: JSON, fmatch: '*.json', fdest: t1.json}
-
-      - name: scan_fmri
-        types: 'Axial fcMRI (EYES OPEN)'
-        resources:
-          - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz}
-          - {resource: JSON, fmatch: '*.json', fdest: fmri.json}
-
-    assessors:
-        - name: assr_fs
-          proctypes: freesurfer720_v2
-          resources:
-            - {resource: SUBJECT, ftype: DIR, fdest: SUBJECT}
-
-    attrs:
-      - {varname: subject, object: session, attr: subject_label}
-      - {varname: session, object: session, attr: label}
-
-outputs:
-  - {path: sourcedata, type: DIR, resource: sourcedata}
-  - {path: HTML, type: DIR, resource: HTML}
-  - {path: BIDS, type: DIR, resource: fmriprepBIDS}
-
-pre:
-  type: singularity_exec
-  container: fmriprep
-  args: >-
-    bash -c '
-    cd /INPUTS &&
-    curl -o v1.5.1.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.5.1.tar.gz &&
-    tar -zxf v1.5.1.tar.gz &&
-    export PATH=/INPUTS/fmriprep-prep-1.5.1/src:\$PATH &&
-    fmriprep-prep.sh
-      --t1_niigz /INPUTS/t1.nii.gz
-      --bids_dir /INPUTS/BIDS
-      --sub {subject}
-      --ses {session}
-      --fmri_niigzs /INPUTS/fmri.nii.gz 
-      --slicetiming Philips_DEFAULT_k
-    '
-
-command:
-  type: singularity_run
-  container: fmriprep
-  args: >-
-    --notrack
-    --output-spaces MNI152NLin2009cAsym
-    --ignore slicetiming
-    --fs-license-file /opt/license.txt
-    /INPUTS/BIDS
-    /OUTPUTS/BIDS
-    participant
-  extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt
-
-post:
-  type: singularity_exec
-  container: fmriprep
-  args: >-
-    bash -c '
-    mkdir /OUTPUTS/HTML &&
-    cp /OUTPUTS/BIDS/sub-*.html /OUTPUTS/HTML &&
-    cp -R /OUTPUTS/BIDS/sub-*/figures /OUTPUTS/HTML/sub-* &&
-    mv /OUTPUTS/BIDS/sourcedata /OUTPUTS/sourcedata
-    '

From b2f9607a9780d98da42e38729ab44b406d6c417f Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Wed, 29 Jan 2025 11:03:06 -0600
Subject: [PATCH 03/10] Update fmriprep-DARBY-philips-def-k_v24.1.1.yaml

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index 2b33ec9..eff9d03 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -1,6 +1,5 @@
 # THIS IS STILL BEING TESTED!!!!!!!!!!!!!!!!!!
 # DON'T USE THIS YET!!!!!!!!!!!!!!!!!!!!!!!!!!
-
 ---
 procyamlversion: 3.0.0-dev.0
 
@@ -88,7 +87,5 @@ post:
     bash -c '
     mkdir /OUTPUTS/HTML &&
     cp /OUTPUTS/BIDS/sub-*.html /OUTPUTS/HTML &&
-    mkdir /OUTPUTS/HTML/sub-* &&
-    cp -R /OUTPUTS/BIDS/sub-*/figures /OUTPUTS/HTML/sub-* &&
-    mv /OUTPUTS/BIDS/sourcedata /OUTPUTS/sourcedata
+    cp -R /OUTPUTS/BIDS/sub-*/figures /OUTPUTS/HTML/sub-* 
     '

From 5300d7eaa5a57174c512e4d1a8fc403129fd0be3 Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Wed, 29 Jan 2025 11:05:32 -0600
Subject: [PATCH 04/10] Update fmriprep-DARBY-philips-def-k_v24.1.1.yaml

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index eff9d03..fbd3edd 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -71,6 +71,7 @@ command:
   type: singularity_run
   container: fmriprep
   args: >-
+    --work-dir /tmp
     --notrack
     --output-spaces MNI152NLin2009cAsym
     --ignore slicetiming

From 8daf114c37df496a11955be982b7bbd665506589 Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Wed, 29 Jan 2025 19:22:46 -0600
Subject: [PATCH 05/10] Update fmriprep-DARBY-philips-def-k_v24.1.1.yaml

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index fbd3edd..b6f65a4 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -81,6 +81,9 @@ command:
     participant
   extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt
 
+# Here we do some extra gymnastics to copy the full HTML output to HTML resource
+# without knowing the dirnames (due to changed subject label). Also, delete the 
+# fsaverage because it just takes up space.
 post:
   type: singularity_exec
   container: fmriprep
@@ -88,5 +91,9 @@ post:
     bash -c '
     mkdir /OUTPUTS/HTML &&
     cp /OUTPUTS/BIDS/sub-*.html /OUTPUTS/HTML &&
-    cp -R /OUTPUTS/BIDS/sub-*/figures /OUTPUTS/HTML/sub-* 
+    cp -R /OUTPUTS/BIDS/sub-* /OUTPUTS/HTML &&
+    rm -fr /OUTPUTS/HTML/sub-*/ses-* &&
+    rm -fr /OUTPUTS/HTML/sub-*/log &&
+    mv /OUTPUTS/BIDS/sourcedata /OUTPUTS/sourcedata &&
+    rm -fr /OUTPUTS/sourcedata/freesurfer/fsaverage
     '

From 0b99e489ab25677ca87f055d28cf160b7b848390 Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Thu, 30 Jan 2025 16:01:23 -0600
Subject: [PATCH 06/10] Update fmriprep-DARBY-philips-def-k_v24.1.1.yaml

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index b6f65a4..f4605cf 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -54,6 +54,8 @@ pre:
   container: fmriprep
   args: >-
     bash -c '
+    mkdir /INPUTS/freesurfer &&
+    mv /INPUTS/SUBJECT/SUBJECT /INPUTS/freesurfer/sub-{subject} &&
     cd /INPUTS &&
     curl -o v1.5.1.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.5.1.tar.gz &&
     tar -zxf v1.5.1.tar.gz &&
@@ -76,6 +78,7 @@ command:
     --output-spaces MNI152NLin2009cAsym
     --ignore slicetiming
     --fs-license-file /opt/license.txt
+    --fs-subjects-dir /INPUTS/freesurfer
     /INPUTS/BIDS
     /OUTPUTS/BIDS
     participant

From a289069ffa0d7478bc052f4ecee366b9dc3909c5 Mon Sep 17 00:00:00 2001
From: Baxter Rogers <baxter.rogers@vanderbilt.edu>
Date: Fri, 31 Jan 2025 07:50:16 -0600
Subject: [PATCH 07/10] no fs

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index f4605cf..771517c 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -85,8 +85,7 @@ command:
   extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt
 
 # Here we do some extra gymnastics to copy the full HTML output to HTML resource
-# without knowing the dirnames (due to changed subject label). Also, delete the 
-# fsaverage because it just takes up space.
+# without knowing the dirnames (due to changed subject label).
 post:
   type: singularity_exec
   container: fmriprep
@@ -96,7 +95,5 @@ post:
     cp /OUTPUTS/BIDS/sub-*.html /OUTPUTS/HTML &&
     cp -R /OUTPUTS/BIDS/sub-* /OUTPUTS/HTML &&
     rm -fr /OUTPUTS/HTML/sub-*/ses-* &&
-    rm -fr /OUTPUTS/HTML/sub-*/log &&
-    mv /OUTPUTS/BIDS/sourcedata /OUTPUTS/sourcedata &&
-    rm -fr /OUTPUTS/sourcedata/freesurfer/fsaverage
+    rm -fr /OUTPUTS/HTML/sub-*/log
     '

From d14909ce2a68e881ac87f334f27888a6a2c37531 Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Mon, 3 Feb 2025 10:37:46 -0600
Subject: [PATCH 08/10] Update fmriprep-DARBY-philips-def-k_v24.1.1.yaml

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index 771517c..6bd1f2e 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -54,8 +54,6 @@ pre:
   container: fmriprep
   args: >-
     bash -c '
-    mkdir /INPUTS/freesurfer &&
-    mv /INPUTS/SUBJECT/SUBJECT /INPUTS/freesurfer/sub-{subject} &&
     cd /INPUTS &&
     curl -o v1.5.1.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.5.1.tar.gz &&
     tar -zxf v1.5.1.tar.gz &&

From 72aeb7dfb52850864f145e66688e4d996938fa53 Mon Sep 17 00:00:00 2001
From: Baxter Rogers <baxter.rogers@vanderbilt.edu>
Date: Tue, 4 Feb 2025 08:12:41 -0600
Subject: [PATCH 09/10] srcdata-gone

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index 771517c..0d2347d 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -45,7 +45,6 @@ inputs:
       - {varname: session, object: session, attr: label}
 
 outputs:
-  - {path: sourcedata, type: DIR, resource: sourcedata}
   - {path: HTML, type: DIR, resource: HTML}
   - {path: BIDS, type: DIR, resource: fmriprepBIDS}
 

From e39b88646ef47ee7172dd6cadabbd2112898fa26 Mon Sep 17 00:00:00 2001
From: duettwe <61516027+duettwe@users.noreply.github.com>
Date: Mon, 17 Feb 2025 08:34:16 -0600
Subject: [PATCH 10/10] Update fmriprep-DARBY-philips-def-k_v24.1.1.yaml

---
 processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
index 88bc755..779e68e 100644
--- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
+++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml
@@ -73,7 +73,6 @@ command:
     --work-dir /tmp
     --notrack
     --output-spaces MNI152NLin2009cAsym
-    --ignore slicetiming
     --fs-license-file /opt/license.txt
     --fs-subjects-dir /INPUTS/freesurfer
     /INPUTS/BIDS