From c6beb86d4f34d88ba6117646c27afefe59983808 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 2 Jul 2018 14:48:25 +0100
Subject: [PATCH] BF: Couple of small tweaks
---
fsl/scripts/extract_noise.py | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/fsl/scripts/extract_noise.py b/fsl/scripts/extract_noise.py
index 5e59493c4..087aceb81 100644
--- a/fsl/scripts/extract_noise.py
+++ b/fsl/scripts/extract_noise.py
@@ -118,6 +118,8 @@ def parseArgs(args):
# Convert confound files to absolute
# paths, error if any do not exist.
+ if args.conffile is None:
+ args.conffile = []
for i, cf in enumerate(args.conffile):
if not op.exists(cf):
print('Confound file does not exist: {}'.format(cf))
@@ -153,8 +155,8 @@ def genComponentIndexList(comps, ncomps):
allcomps.extend([c - 1 for c in ccomps])
- if any([cc < 0 or cc >= ncomps for cc in ccomps]):
- raise ValueError('Invalid component indices: {}'.format(ccomps))
+ if any([c < 0 or c >= ncomps for c in allcomps]):
+ raise ValueError('Invalid component indices: {}'.format(allcomps))
return list(sorted(set(allcomps)))
@@ -214,12 +216,13 @@ def main(argv=None):
args = parseArgs(argv)
try:
- comps = genComponentIndexList(args.components)
- ts = melanalysis.getComponentTimeSeries(args.icadir)
- ts = ts[:, comps]
- confs = loadConfoundFiles(args.conffiles, ts.shape[0])
+ ts = melanalysis.getComponentTimeSeries(args.icadir)
+ npts, ncomps = ts.shape
+ confs = loadConfoundFiles(args.conffile, npts)
+ comps = genComponentIndexList(args.components, ncomps)
+ ts = ts[:, comps]
- except ValueError as e:
+ except Exception as e:
print(e)
sys.exit(1)
--
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