From c076b51bff53f7c101eda922b597b8b312714e92 Mon Sep 17 00:00:00 2001
From: slimnsour <slimnsour@gmail.com>
Date: Thu, 20 Oct 2022 16:27:58 -0400
Subject: [PATCH] Minor changes to coordinate delimiter, ciftify container
 binding

---
 modules/cifti_mesh_wf.nf  | 4 +++-
 modules/transformation.nf | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/cifti_mesh_wf.nf b/modules/cifti_mesh_wf.nf
index 1e4a7c3..2d7e2e1 100644
--- a/modules/cifti_mesh_wf.nf
+++ b/modules/cifti_mesh_wf.nf
@@ -108,6 +108,8 @@ process ciftify{
     -v !{params.bids}:/bids \
     -v $(pwd):/output \
     -v $(pwd)/work:/work \
+    -v $(pwd)/fmriprep:/fmriprep \
+    -v $(pwd)/freesurfer:/freesurfer \
     -v !{params.license}:/license \
     -v !{params.resources}:/resources \
     !{params.ciftify_descriptor} $(pwd)/!{json} \
@@ -470,7 +472,7 @@ workflow cifti_meshing_wf {
 
         mri2mesh(
         fmriprep_anat_wf.out.preproc_t1.map { s, t1 ->
-            [ s, t1, try_fetch_t2("${params.bids}/${s}/**/*T2w.nii.gz") ]
+            [ s, t1, try_fetch_t2("${params.bids}/${s}/*/*/*T2w.nii.gz") ]
         })
 
         // Full fmriprep/ciftify pipeline
diff --git a/modules/transformation.nf b/modules/transformation.nf
index 0067539..5168f6a 100644
--- a/modules/transformation.nf
+++ b/modules/transformation.nf
@@ -107,7 +107,7 @@ process format_for_ants {
     import numpy as np
 
     # Read in RAS, convert to LPS
-    coords = np.loadtxt('${coords}', delimiter=',')
+    coords = np.loadtxt('${coords}', delimiter=' ')
     coords[0] = -coords[0]
     coords[1] = -coords[1]