Skip to content

use orig or tlrc anat_final scans for qc image #12

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
leej3 wants to merge 2 commits into
base: master
Choose a base branch
from
Open

use orig or tlrc anat_final scans for qc image #12

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f29cc48
use orig or tlrc anat_final scans for qc image
leej3 May 31, 2018
7a14e4a
undo dockerfile changes
leej3 May 31, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ ENV LANG="en_US.UTF-8" \
AFNI_NIFTI_VIEW="orig"

RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
apt-utils bzip2 ca-certificates curl locales unzip \
apt-utils bzip2 ca-certificates curl locales unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& localedef --force --inputfile=en_US --charmap=UTF-8 C.UTF-8 \
Expand Down
4 changes: 3 additions & 1 deletion run.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python3
#!/usr/bin/env python3
from __future__ import absolute_import, division, print_function, unicode_literals

import argparse
Expand Down Expand Up @@ -381,6 +381,8 @@ def run(command, env={}, shell=False):
try:

anat_out_path = os.path.join(task_out_dir, 'anat_final.%s+tlrc.HEAD'%subject_label)
if not os.path.exists(anat_out_path):
anat_out_path = os.path.join(task_out_dir, 'anat_final.%s+orig.HEAD'%subject_label)
anat_exts = np.array([float(ss) for ss in subprocess.check_output(["3dinfo", "-extent", anat_out_path]).decode().split('\t')])
anat_lrext = np.abs(anat_exts[0]) + np.abs(anat_exts[1])
anat_mont_dim = np.floor(np.sqrt(anat_lrext))
Expand Down