From 0c4b3210db11b2118a0a7aca68f8734e93fc24f9 Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Wed, 22 Feb 2023 18:32:02 +0000
Subject: [PATCH] Adding new IDP generation scripts
---
bip/data/IDPs/GMatlas/GMatlas.nii.gz | 3 ++
bip/data/IDPs/GMatlas/GMatlas.sh | 3 ++
bip/data/IDPs/GMatlas/GMatlas.txt | 3 ++
bip/data/IDPs/GMatlas/labels.txt | 3 ++
.../IDPs_gen/IDP_T1_GM_parcellation.py | 43 +++++++++++++++++++
bip/pipelines/IDPs_gen/IDP_func_TSNR.py | 5 +--
6 files changed, 56 insertions(+), 4 deletions(-)
create mode 100644 bip/data/IDPs/GMatlas/GMatlas.nii.gz
create mode 100644 bip/data/IDPs/GMatlas/GMatlas.sh
create mode 100755 bip/data/IDPs/GMatlas/GMatlas.txt
create mode 100644 bip/data/IDPs/GMatlas/labels.txt
create mode 100755 bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
diff --git a/bip/data/IDPs/GMatlas/GMatlas.nii.gz b/bip/data/IDPs/GMatlas/GMatlas.nii.gz
new file mode 100644
index 0000000..59fec49
--- /dev/null
+++ b/bip/data/IDPs/GMatlas/GMatlas.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5c4d35577cb6297eec0a49218441eea50285869375c66617864f9f0fddb52d58
+size 306998
diff --git a/bip/data/IDPs/GMatlas/GMatlas.sh b/bip/data/IDPs/GMatlas/GMatlas.sh
new file mode 100644
index 0000000..b4e86d3
--- /dev/null
+++ b/bip/data/IDPs/GMatlas/GMatlas.sh
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d7a1b0229c087bdcba1cf75ec75f48abdfcbdda1fb4a878c557c0a0c8d0917ad
+size 1016
diff --git a/bip/data/IDPs/GMatlas/GMatlas.txt b/bip/data/IDPs/GMatlas/GMatlas.txt
new file mode 100755
index 0000000..eb76bce
--- /dev/null
+++ b/bip/data/IDPs/GMatlas/GMatlas.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f84489d6566cbe06a7f87e2ff18295724831235926d981f2ac04d63c8afb781b
+size 4292
diff --git a/bip/data/IDPs/GMatlas/labels.txt b/bip/data/IDPs/GMatlas/labels.txt
new file mode 100644
index 0000000..603705c
--- /dev/null
+++ b/bip/data/IDPs/GMatlas/labels.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fe46839159b64914092c5c401e28142cfdb9aac20c30a367433985eed01e95dc
+size 2547
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py b/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
new file mode 100755
index 0000000..2fe4efd
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+#
+# IDP_T1_GM_parcellation.py - Generating IDP file with GM parcellation metrics
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from fsl import wrappers
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging, tempdir
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ T1: In,
+ T1_to_MNI_warp_coef_inv: In,
+ T1_fast_pve_1: In,
+ logs_dir: Ref,
+ IDP_T1_GM_parcellation: Out):
+
+ with redirect_logging('IDP_T1_GM_parcellation', outdir=logs_dir),\
+ tempdir(tmp_dir):
+ result = ("NaN " * 139).strip()
+
+ GMatlas_to_T1 = tmp_dir + '/GMatlas_to_T1.nii.gz'
+ GMatlas = ctx.get_data("IDPs/GMatlas/GMatlas.nii.gz")
+
+ wrappers.applywarp(src=GMatlas, ref=T1, w=T1_to_MNI_warp_coef_inv,
+ out=GMatlas_to_T1, interp='nn')
+
+ wrappers.fslstats(fMRI_SNR).l(0.1).p(50).run()
+ vals = wrappers.fslstats(T1_brain_pve_1, K=GMatlas_to_T1).m.v.run()
+ result = " ".join([str(x) for x in vals[:,0] * vals[:,1]])
+
+ with open(IDP_T1_GM_parcellation, 'wt', encoding="utf-8") as f:
+ f.write(f'{result}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
index 92e0b3f..1a88090 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
@@ -38,10 +38,7 @@ def run(ctx,
if os.path.exists(file_name):
wrappers.fslmaths(file_name).Tstd().run(fMRI_SNR)
wrappers.fslmaths(file_name).Tmean().div(fMRI_SNR).run(fMRI_SNR)
- v=wrappers.fslstats(fMRI_SNR).l(0.1).p(50).run()
- print(v)
- v = 1/v
- print(v)
+ v = 1 / wrappers.fslstats(fMRI_SNR).l(0.1).p(50).run()
result += f"{v} "
else:
result += "NaN "
--
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