diff --git a/.gitignore b/.gitignore
index 3fe5323ae0f08e6ac7a4741d9d168358822a545a..365008ab678f6d9b5d619f708cabea6247c8a3f3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,8 @@ __pycache__/
# Distribution / packaging
.Python
+TODOs
+PendingTasks
build/
obsolete/
structure
diff --git a/bip/ext_wrappers/__init__.py b/bip/ext_wrappers/__init__.py
deleted file mode 100755
index 685f904fbf475979d62409f401c445ca7b21c06c..0000000000000000000000000000000000000000
--- a/bip/ext_wrappers/__init__.py
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env python
-#
-# pylint: disable=unused-import
-# flake8: noqa: F401
-#
-# __init__.py - Wrappers for external command-line tools.
-#
-# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
-#
-"""This package contains wrappers for various command line tools, allowing
-them to be called from Python.
-"""
-
-from bip.ext_wrappers.freesurfer import (recon_all,
- asegstats2table,
- aparcstats2table)
diff --git a/bip/ext_wrappers/freesurfer.py b/bip/ext_wrappers/freesurfer.py
deleted file mode 100644
index 8cfb1a883ad638cb3d70eb7c53106c01ddd63f8f..0000000000000000000000000000000000000000
--- a/bip/ext_wrappers/freesurfer.py
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-#
-# freesurfer.py - Wrappers for FreeSurfer and its sub-functions
-#
-# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
-#
-"""This module provides wrapper functions for FreeSurfer
-
-"""
-
-import os
-import fsl.utils.assertions as asrt
-from fsl.wrappers import wrapperutils as wutils
-
-
-import sys
-
-def eprint(*args, **kwargs):
- print(*args, file=sys.stderr, **kwargs)
-
-
-@wutils.fileOrImage('infile')
-@wutils.cmdwrapper
-def recon_all(subjects_dir, directive, subjid, infile, FLAIR=None, **kwargs):
- """Wrapper for the ``recon-all`` command.
- """
- #asrt.assertIsNifti(*infile)
-
- os.environ["SUBJECTS_DIR"] = subjects_dir
-
- cmd = ['recon-all', "-" + directive + " -s " + subjid]
- cmd += [" -i " + subjects_dir + "/" + infile]
-
- if FLAIR:
- cmd += [" -FLAIR " + subjects_dir + "/" + FLAIR + " -FLAIRpial -debug"]
-
- return cmd
-
-@wutils.cmdwrapper
-def asegstats2table(subjects_dir, mask, tablefile, subjects, **kwargs):
- """Wrapper for the ``asegstats2table`` command.
- """
- os.environ["SUBJECTS_DIR"] = subjects_dir
- cmd = ['asegstats2table']
-
- return cmd
-
-@wutils.cmdwrapper
-def aparcstats2table(subjects_dir, mask, tablefile, subjects, hemi, atlas,
- **kwargs):
- """Wrapper for the ``aparcstats2table`` command.
- """
- os.environ["SUBJECTS_DIR"] = subjects_dir
- cmd = ['aparcstats2table']
-
- return cmd
diff --git a/bip/main.py b/bip/main.py
index 55ccda19aa978e844f81a8dc3510c33c2a083069..ab6ef498f3e84a658386b7d34db30310040d642c 100755
--- a/bip/main.py
+++ b/bip/main.py
@@ -7,7 +7,7 @@
'''
import os
-import os.path
+import os.path as op
import sys
import logging
import argparse
@@ -42,7 +42,7 @@ class Context:
FSLDIR: str = os.environ['FSLDIR']
gdc: str = field(init=False)
- with open(BB_BIN_DIR + '/data/dMRI/autoptx/struct_list.json', 'r') as f:
+ with open(self.get_data('dMRI/autoptx/struct_list.json'), 'r') as f:
tract_struct = json.load(f)
def __post_init__(self):
@@ -50,20 +50,26 @@ class Context:
@property
def MNI(self):
- return self.FSLDIR + '/data/standard/MNI152_T1_1mm'
+ return self.get_standard('MNI152_T1_1mm')
@property
def MNI_brain_mask(self):
- return self.FSLDIR + '/data/standard/MNI152_T1_1mm_brain_mask'
+ return self.get_standard('MNI152_T1_1mm_brain_mask')
def get_standard(self, fileName):
- return self.FSLDIR + '/data/standard/' + fileName
+ fileName.replace('/', os.sep)
+ basedir = self.FSLDIR + os.sep + op.foin('data', 'standard') + os.sep
+ return basedir + fileName
def get_atlas(self, fileName):
- return self.FSLDIR + '/data/atlases/' + fileName
+ fileName.replace('/', os.sep)
+ basedir = self.FSLDIR + os.sep + op.foin('data', 'atlases') + os.sep
+ return basedir + fileName
def get_data(self, fileName):
- return self.BB_BIN_DIR + '/data/' + fileName
+ fileName.replace('/', os.sep)
+ basedir = self.BB_BIN_DIR + os.sep + 'data' + os.sep
+ return basedir + fileName
#def save_context(self, file_name):
# with open(file_name, "wt") as config_file:
@@ -160,7 +166,7 @@ def parseArguments(ctx):
if coeff == "":
coeff = "skyra"
if coeff not in ["skyra", "prisma", "none"]:
- if not os.path.exists(coeff):
+ if not op.exists(coeff):
log.error("ERROR: Subject cannot be run. Incorrect GDC file specified: " +
coeff)
sys.exit(1)
@@ -170,7 +176,7 @@ def parseArguments(ctx):
coeff = ctx.get_data("GDC/bb_GDC_coeff_skyra.grad")
elif coeff == "prisma":
coeff = ctx.get_data("GDC/bb_GDC_coeff_prisma.grad")
- if not os.path.exists(coeff):
+ if not op.exists(coeff):
coeff = "none"
# Parsing number of SWI coils argument
@@ -247,7 +253,7 @@ def parseArguments(ctx):
naming_patterns = argsa.naming_patterns
naming_patterns = naming_patterns.strip()
- if not os.path.exists(naming_patterns):
+ if not op.exists(naming_patterns):
log.error("ERROR: Subject cannot be run. Incorrect naming pattern file specified: " +
naming_patterns)
sys.exit(1)
@@ -258,23 +264,23 @@ def parseArguments(ctx):
B_files = B_files.strip()
if B_files != "":
- if not os.path.exists(B_files):
+ if not op.exists(B_files):
log.error("ERROR: Subject cannot be run. Incorrect B-files directory specified: " +
B_files)
sys.exit(1)
else:
for fil in ["AP.bval", "AP.bvec" , "PA.bval", "PA.bvec"]:
- if not os.path.exists(B_files + '/' + fil ):
+ if not op.exists(op.join(B_files, fil)):
log.error("ERROR: Subject cannot be run. Non-existent B-file: " +
- B_files + '/' + fil )
+ op.join(B_files, fil) )
sys.exit(1)
- if not os.path.isabs(B_files):
- B_files = os.path.abspath(B_files)
+ if not op.isabs(B_files):
+ B_files = op.abspath(B_files)
# Parsing basic QC file argument
basic_QC_file = argsa.basic_QC_file
basic_QC_file = basic_QC_file.strip()
- if not os.path.exists(basic_QC_file):
+ if not op.exists(basic_QC_file):
log.error("ERROR: Subject cannot be run. Incorrect basic QC file specified: " +
basic_QC_file)
sys.exit(1)
@@ -312,7 +318,7 @@ def main():
parseArguments(ctx)
- setup_logging(ctx.subject + '/logs/main.log')
+ setup_logging(op.join(ctx.subject, 'logs', 'main.log'))
tree = FileTree.read(ctx.get_data('FileTree'),
subject=ctx.subject,
diff --git a/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py b/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
index 4226a1e1818d3a9d8af4d170e0b96fb7f6909e6d..910599531a2446157172fd92ca2a2b1465620529 100755
--- a/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
+++ b/bip/pipelines/IDPs_gen/IDP_SWI_T2star.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -28,7 +29,7 @@ def run(ctx,
result = ("NaN " * 14).strip()
- if os.path.exists(T1_first_all_fast_firstseg):
+ if op.exists(T1_first_all_fast_firstseg):
v=wrappers.fslstats(T2star_to_T1, K=T1_first_all_fast_firstseg).p(50).run()
# Check that the outputs are OK
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
index 28d1fa2318836e91d8c94d541b5d3c87a438a808..3aed0f4ea9919bf7c5d6446cd396f95f43500471 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -26,7 +27,7 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
result = ("NaN " * 15).strip()
- if os.path.exists(T1_first_all_fast_firstseg):
+ if op.exists(T1_first_all_fast_firstseg):
v=wrappers.fslstats(T1_first_all_fast_firstseg).H(58,0.5,58.5).run()
# Check that the outputs are OK
if len(v) == 58:
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py b/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
index d810c588faa7b18c35ba560688df14ef513ec172..e746cf73b46e0bc9d667f6ac29ce30bc3e03515f 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_GM_parcellation.py
@@ -9,6 +9,7 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -25,10 +26,11 @@ def run(ctx,
IDP_T1_GM_parcellation: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
+
result = ("NaN " * 139).strip()
- GMatlas_to_T1 = tmp_dir + '/GMatlas_to_T1.nii.gz'
+ GMatlas_to_T1 = op.join(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,
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
index 02af2ef2a5f09e89d1655d0a99c86fd157da518d..bf275eb27d6ad57be80189fd2ce190546cb3f55e 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
@@ -28,7 +29,7 @@ def run(ctx,
result = ("NaN " * 11).strip()
- if os.path.exists(T1_sienax_report):
+ if op.exists(T1_sienax_report):
with open(T1_sienax_report, "r", encoding="utf-8") as f:
text = f.readlines()
# indices that we are interested in
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py b/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
index 92f265dbe07badd13982fbd0cf2e67a1b9902af1..c598f210e92a0a1c3392cef2cd38ae5e44422792 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_align_to_std.py
@@ -9,6 +9,7 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -26,12 +27,12 @@ def run(ctx,
IDP_T1_align_to_std: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- tmp_jac = tmp_dir + '/tmpjac.nii.gz'
- tmp_mat = tmp_dir + '/tmp_mat.mat'
+ tmp_jac = op.join(tmp_dir, 'tmpjac.nii.gz')
+ tmp_mat = op.join(tmp_dir, 'tmp_mat.mat')
- MC=ctx.FSLDIR + '/etc/flirtsch/measurecost1.sch'
+ MC=ctx.FSLDIR + '/etc/flirtschop.join(tmp_dir, 'op.join(tmp_dir, 'measurecost1.sch'
MNI152_T1_1mm_brain = ctx.get_standard("MNI152_T1_1mm_brain.nii.gz")
MNI152_T1_1mm_brain_mask = ctx.get_standard("MNI152_T1_1mm_brain_mask.nii.gz")
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py b/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py
index eb8dc9e64ca33ce02e461dc455fb8c1d86a83222..90b1b6b1ec8cce86f6ef8587f0bb0d03ff3a9c36 100755
--- a/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py
+++ b/bip/pipelines/IDPs_gen/IDP_T1_noise_ratio.py
@@ -10,6 +10,7 @@
# pylint: disable=W0613
#
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -25,9 +26,9 @@ def run(ctx,
IDP_T1_noise_ratio: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- tmp_SNR = tmp_dir + '/tmp_SNR.nii.gz'
+ tmp_SNR = op.join(tmp_dir, 'tmp_SNR.nii.gz')
wrappers.fslmaths(T1_fast_pveseg).thr(2).uthr(2).ero().run(tmp_SNR)
grey = wrappers.fslstats(T1).k(tmp_SNR).m.run()
diff --git a/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py b/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
index ace1ba26773ca580a6a6c78cd5ba8cc1ef2813ae..dbfac5e3cda68d783157633fdc5e3f949cba1a43 100755
--- a/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
+++ b/bip/pipelines/IDPs_gen/IDP_all_align_to_T1.py
@@ -10,6 +10,7 @@
#
import os
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -30,18 +31,18 @@ def run(ctx,
IDP_all_align_to_T1: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- tmp_mat = tmp_dir + '/tmp_mat.mat'
+ tmp_mat = op.join(tmp_dir, 'tmp_mat.mat')
result=""
- MC=ctx.FSLDIR + '/etc/flirtsch/measurecost1.sch'
+ MC = op.join(ctx.FSLDIR, 'etc', 'flirtsch', 'measurecost1.sch')
for file_name in [T2_FLAIR_brain, fieldmap_iout_to_T1, SWI_to_T1,
rfMRI_example_func2highres,tfMRI_example_func2highres]:
- if os.path.exists(file_name):
+ if op.exists(file_name):
costs1 = wrappers.flirt(src=file_name, ref=T1_brain,
refweight=T1_brain_mask, schedule=MC,
omat=tmp_mat).stdout[0].strip()
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
index c5f60043317792461ff8072ad19524f38bd0b35f..b12d1c2ec2c63c84b3137e56f1cd227edef05ad6 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging, job_name
@@ -33,7 +34,7 @@ def run(ctx,
file_name = JHUrois_prefix + mod + ".txt"
print(file_name)
- if os.path.exists(file_name):
+ if op.exists(file_name):
with open(file_name, "r", encoding="utf-8") as f:
mini_result = f.read()
mini_result = mini_result.replace("\n", " ")
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
index fece943161cd2957c74932bbd7f65dc5dc04a605..eb2751059a8d7d0b0ae29e60da92aa8d1e3ae348 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
import nibabel as nib
from fsl import wrappers
@@ -29,10 +30,10 @@ def run(ctx,
IDP_diff_autoPtx: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir + "/" + __name__):
+ tempdir(op.join(tmp_dir, job_name(run))):
- autoPtx_all = tmp_dir + '/autoPtx_all.nii.gz'
- autoPtx_tmp = tmp_dir + '/autoPtx_tmp.nii.gz'
+ autoPtx_all = op.join(tmp_dir, 'autoPtx_all.nii.gz')
+ autoPtx_tmp = op.join(tmp_dir, 'autoPtx_tmp.nii.gz')
result_NaN = ("NaN " * 27).strip()
result = ""
@@ -45,7 +46,7 @@ def run(ctx,
all_file = TBSS_prefix + suffix + ".nii.gz"
APTX_file = aptx_txt_prefix + suffix + ".txt"
- if os.path.exists(all_file):
+ if op.exists(all_file):
wrappers.fslmaths(autoPtx_all).mul(all_file).run(autoPtx_tmp)
tractmeas = wrappers.fslstats(autoPtx_tmp, t=True).m.run()
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
index 6514adbfd733eb4d3a34e8136a03b0f5fbdfd3da..a27c5d7352fd01487cd57fb15ce047ffab6add0a 100755
--- a/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
+++ b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging, job_name
@@ -26,7 +27,7 @@ def run(ctx,
num_outliers = 0
- if os.path.exists(eddy_outlier_report):
+ if op.exists(eddy_outlier_report):
with open(eddy_outlier_report, "r", encoding="utf-8") as f:
num_outliers = str(len(f.readlines()))
else:
diff --git a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
index 249417dbdfe78bd32abb077f78c4ec66edc2a40d..9c68babe0a713b051f0510feceaf930c7f8be915 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
@@ -27,15 +28,15 @@ def run(ctx,
IDP_func_TSNR: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- fMRI_SNR = tmp_dir + '/fMRI_SNR.nii.gz'
+ fMRI_SNR = op.join(tmp_dir, 'fMRI_SNR.nii.gz')
result =""
for file_name in [filtered_func_data, filtered_func_data_clean,
tfMRI_filtered_func_data]:
- if os.path.exists(file_name):
+ if op.exists(file_name):
wrappers.fslmaths(file_name).Tstd().run(fMRI_SNR)
wrappers.fslmaths(file_name).Tmean().div(fMRI_SNR).run(fMRI_SNR)
v = 1 / wrappers.fslstats(fMRI_SNR).l(0.1).p(50).run()
diff --git a/bip/pipelines/IDPs_gen/IDP_func_head_motion.py b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
index 8bf3a0c4fd827d6b148df4b5340cec67db44d4d3..ec5c137c5f89bbfa002ecc34bb47c947c3dab939 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import json
import logging
from pipe_tree import In, Out, Ref
@@ -26,13 +27,13 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- if os.path.exists(rfMRI_mc_rel_mean):
+ if op.exists(rfMRI_mc_rel_mean):
with open(rfMRI_mc_rel_mean, "r", encoding="utf-8") as f:
val_1 = json.load(f)
else:
val_1 = "NaN"
- if os.path.exists(tfMRI_mc_rel_mean):
+ if op.exists(tfMRI_mc_rel_mean):
with open(tfMRI_mc_rel_mean, "r", encoding="utf-8") as f:
val_2 = json.load(f)
else:
diff --git a/bip/pipelines/IDPs_gen/IDP_func_task_activation.py b/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
index d0263354325f6c4069882ac1b3525d1e34727bc6..c713241c476909a4a10c8b23714d22f5fcefc734 100755
--- a/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
+++ b/bip/pipelines/IDPs_gen/IDP_func_task_activation.py
@@ -10,6 +10,7 @@
#
import os
+import os.path as op
import shutil
import logging
from fsl import wrappers
@@ -42,17 +43,19 @@ def run(ctx,
IDP_func_task_activation: Out):
with redirect_logging(job_name(run), outdir=logs_dir):
- if not os.path.exists(highres2standard_warp):
- os.symlink(src=os.getcwd() + "/" + T1_to_MNI_warp,
- dst=highres2standard_warp)
+
+ if not op.exists(highres2standard_warp):
+ rel_path = op.relpath(T1_to_MNI_warp, highres2standard_warp)
+ os.symlink(src=rel_path, dst=highres2standard_warp)
- if not os.path.exists(highres2standard_warp_inv):
- os.symlink(src=os.getcwd() + "/" + T1_to_MNI_warp_coef_inv,
- dst=highres2standard_warp_inv)
+ if not op.exists(highres2standard_warp_inv):
+ rel_path = op.relpath(T1_to_MNI_warp_coef_inv,
+ highres2standard_warp_inv)
+ os.symlink(src=rel_path, dst=highres2standard_warp_inv)
for dir_name in [tfMRI_featquery_1_dir, tfMRI_featquery_2_dir,
tfMRI_featquery_5_dir, tfMRI_featquery_5a_dir]:
- if os.path.exists(dir_name):
+ if op.exists(dir_name):
shutil.rmtree(dir_name)
group_mask_1 = ctx.get_data("tfMRI_group/groupMask1.nii.gz")
@@ -60,7 +63,7 @@ def run(ctx,
group_mask_5 = ctx.get_data("tfMRI_group/groupMask5.nii.gz")
group_mask_5a = ctx.get_data("tfMRI_group/groupMask5a.nii.gz")
- tfMRI_feat += "/"
+ tfMRI_feat += os.sep
N_tfMRI_cope1 = tfMRI_cope1.replace(tfMRI_feat, "")
N_tfMRI_cope2 = tfMRI_cope2.replace(tfMRI_feat, "")
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
index 94ddb79cf2112de177eadad4cd50b93361594893..ef09016ce0c751782d74a55cdcb53f291a19813f 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from pipe_tree import In, Out, Ref
from bip.utils.log_utils import redirect_logging, job_name
@@ -39,7 +40,7 @@ def run(ctx,
for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
dMRI_dcm_txt, tfMRI_dcm_txt]:
- if os.path.exists(file_name):
+ if op.exists(file_name):
with open(file_name, 'rt', encoding="utf-8") as f:
cont = f.readlines()
for x in cont:
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_centre.py b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
index 80a077c493d0f600336fcca22401b4cad052662b..c18932409b999891e822b8adafd5d5bfcf97e473 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_centre.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
@@ -10,6 +10,7 @@
#
import os
+import os.path as op
import json
import logging
from pipe_tree import In, Out, Ref
@@ -35,7 +36,7 @@ def run(ctx,
for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
dMRI_dcm_txt, tfMRI_dcm_txt]:
- if os.path.exists(file_name):
+ if op.exists(file_name):
with open(file_name, 'rt', encoding="utf-8") as f:
cont = f.readlines()
diff --git a/bip/pipelines/IDPs_gen/IDPs_generator.py b/bip/pipelines/IDPs_gen/IDPs_generator.py
index 9e7c9ca0050b7ca14ad61ffc9e62556eaf8d0958..a4ba81554d3f6ed4bbb79e724b850b5f46c6afe6 100755
--- a/bip/pipelines/IDPs_gen/IDPs_generator.py
+++ b/bip/pipelines/IDPs_gen/IDPs_generator.py
@@ -10,6 +10,7 @@
#
import os
+import os.path as op
import json
import logging
from pipe_tree import In, Out, Ref
@@ -53,11 +54,11 @@ def run(ctx,
IDP_func_task_activation, IDP_diff_TBSS, IDP_diff_autoPtx,
IDP_subject_COG_table, IDP_subject_centre]:
- plain_name = os.path.basename(IDP_file).replace(".txt", "")
+ plain_name = op.basename(IDP_file).replace(".txt", "")
num_IDPs = len(IDPs_dict[plain_name])
result_nans = ("NaN " * num_IDPs).strip()
- if os.path.exists(IDP_file):
+ if op.exists(IDP_file):
with open(IDP_file, "r", encoding="utf-8") as f:
IDPs_l = f.read().strip().split()
if len(IDPs_l) != num_IDPs:
diff --git a/bip/pipelines/dMRI_diff/diff_autoptx.py b/bip/pipelines/dMRI_diff/diff_autoptx.py
index 6b2629bee19917d9a5a6bf00bad267acc873398e..adc53b83c8b122068baa8e8ba94f2d021729743b 100755
--- a/bip/pipelines/dMRI_diff/diff_autoptx.py
+++ b/bip/pipelines/dMRI_diff/diff_autoptx.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import random
import logging
from shutil import copyfile
@@ -54,9 +55,9 @@ def run(ctx,
# Does the protocol defines a second
# run with inverted seed / target masks?
- if os.path.exists(orig_tract_dir + 'invert'):
+ if op.exists(orig_tract_dir + 'invert'):
symtrack=True
- if os.path.exists(waytotal):
+ if op.exists(waytotal):
os.remove(waytotal)
else:
symtrack=False
@@ -66,7 +67,7 @@ def run(ctx,
copyfile(orig_tract_dir + 'target.nii.gz', aptx_target)
copyfile(orig_tract_dir + 'exclude.nii.gz', aptx_exclude)
- if os.path.exists(waytotal):
+ if op.exists(waytotal):
os.remove(waytotal)
# Building arguments dictionary for probtrackx
@@ -87,7 +88,7 @@ def run(ctx,
# Is there a stop criterion defined
# in the protocol for this struct?
- if os.path.exists(orig_tract_dir + 'stop.nii.gz'):
+ if op.exists(orig_tract_dir + 'stop.nii.gz'):
kwargs['stop'] = aptx_stop
copyfile(orig_tract_dir + 'stop.nii.gz', aptx_stop)
@@ -115,7 +116,7 @@ def run(ctx,
way1 = int(f.read())
with open(waytotal_inv, 'r', encoding="utf-8") as f:
way2 = int(f.read())
- if os.path.exists(waytotal):
+ if op.exists(waytotal):
os.remove(waytotal)
with open(waytotal, 'wt', encoding="utf-8") as f:
way = way1 + way2
diff --git a/bip/pipelines/dMRI_diff/diff_bedpostx.py b/bip/pipelines/dMRI_diff/diff_bedpostx.py
index 8b4aab4b60d3b31a17460361bd2d68e8e781c790..0fabdf158e105304f2ec4da31152e3c8ba6736e6 100755
--- a/bip/pipelines/dMRI_diff/diff_bedpostx.py
+++ b/bip/pipelines/dMRI_diff/diff_bedpostx.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
from fsl import wrappers
@@ -40,14 +41,15 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- w = os.getcwd() + "/"
+ w = os.getcwd() + os.sep
# Copy of bvals and bvecs
copyfile(src=AP_bval, dst=bedpostx_bvals)
copyfile(src=AP_bvec, dst=bedpostx_bvecs)
copyfile(src=eddy_nodif_brain_mask, dst=bedpostx_nodif_brain_mask)
- wrappers.fslmaths(eddy_nodif).mas(eddy_nodif_brain_mask).run(bedpostx_nodif_brain)
+ wrappers.fslmaths(eddy_nodif).mas(eddy_nodif_brain_mask).\
+ run(bedpostx_nodif_brain)
nvox=wrappers.fslstats(bedpostx_nodif_brain_mask).V.run()[0]
with open(bedpostx_nvox, 'wt', encoding="utf-8") as f:
@@ -81,5 +83,5 @@ def run(ctx,
SubjectDir=w + eddy_dir,
TotalNumParts="1", bindir=ctx.FSLDIR)
- if os.path.exists(bedpostx_data_0):
+ if op.exists(bedpostx_data_0):
os.remove(bedpostx_data_0)
diff --git a/bip/pipelines/dMRI_diff/diff_dtifit.py b/bip/pipelines/dMRI_diff/diff_dtifit.py
index ea4cc46f2611c0a43e9f5b3ba979cd0f24fb9b0c..a6a900e8b8d01745b004aaf3c5b51b4a75da6370 100755
--- a/bip/pipelines/dMRI_diff/diff_dtifit.py
+++ b/bip/pipelines/dMRI_diff/diff_dtifit.py
@@ -10,6 +10,7 @@
# pylint: disable=W0613
#
+import os.path as op
import logging
from shutil import copyfile
import numpy as np
diff --git a/bip/pipelines/dMRI_diff/diff_eddy.py b/bip/pipelines/dMRI_diff/diff_eddy.py
index a47794e9a85c59414fa8b71ae7c2357f0dd011cf..38d160cbc63bb6b27d30ba7d4a9b95d7c65d8044 100755
--- a/bip/pipelines/dMRI_diff/diff_eddy.py
+++ b/bip/pipelines/dMRI_diff/diff_eddy.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
import nibabel as nib
@@ -47,14 +48,18 @@ def run(ctx,
# Creates links
# TODO: These links are NOT relative. This may cause future problems.
- if not os.path.exists(eddy_AP):
- os.symlink(src="../../../" + AP, dst=eddy_AP)
- if not os.path.exists(eddy_nodif):
- os.symlink(src="../../../" + fieldmap_iout_mean, dst=eddy_nodif)
- if not os.path.exists(eddy_nodif_brain_mask):
- os.symlink(src="../../../" + fieldmap_mask, dst=eddy_nodif_brain_mask)
- if not os.path.exists(eddy_nodif_brain_mask_ud):
- os.symlink(src="../../../" + fieldmap_mask_ud, dst=eddy_nodif_brain_mask_ud)
+ if not op.exists(eddy_AP):
+ rel_path = op.relpath(AP, eddy_AP)
+ os.symlink(src=rel_path, dst=eddy_AP)
+ if not op.exists(eddy_nodif):
+ rel_path = op.relpath(fieldmap_iout_mean, eddy_nodif)
+ os.symlink(src=rel_path, dst=eddy_nodif)
+ if not op.exists(eddy_nodif_brain_mask):
+ rel_path = op.relpath(fieldmap_mask, eddy_nodif_brain_mask)
+ os.symlink(src=rel_path, dst=eddy_nodif_brain_mask)
+ if not op.exists(eddy_nodif_brain_mask_ud):
+ rel_path = op.relpath(fieldmap_mask_ud, eddy_nodif_brain_mask_ud)
+ os.symlink(src=rel_path, dst=eddy_nodif_brain_mask_ud)
copyfile(src=AP_bval, dst=eddy_bvals)
copyfile(src=AP_bvec, dst=eddy_bvecs)
diff --git a/bip/pipelines/dMRI_diff/diff_noddi.py b/bip/pipelines/dMRI_diff/diff_noddi.py
index 1ef59a233b8526bea52291ef5325d79eb1f7e84b..95e6c5d9cce63d4258d6b985318fc9def12ec5e9 100755
--- a/bip/pipelines/dMRI_diff/diff_noddi.py
+++ b/bip/pipelines/dMRI_diff/diff_noddi.py
@@ -10,6 +10,7 @@
#
import os
+import os.path as op
import logging
from shutil import move, rmtree
import zipfile
@@ -39,16 +40,18 @@ def run(ctx,
NODDI_dir_file: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
- amtmp = tmp_dir + '/amtmp.nii'
- amtmp_mask = tmp_dir + '/amtmp_mask.nii'
+ tempdir(op.join(tmp_dir, job_name(run))):
+
+ amtmp = op.join(tmp_dir, 'amtmp.nii')
+ amtmp_mask = op.join(tmp_dir, 'amtmp_mask.nii')
# In case the kernels were already calculated for this study:
# TODO: Verify that this is regular UKB data.
# Otherwise, this should not be done
- if not os.path.exists('./kernels/'):
- if os.path.exists(ctx.get_data('dMRI/kernels.zip')):
- with zipfile.ZipFile(ctx.get_data('dMRI/kernels.zip'), 'r') as zip_ref:
+ if not op.exists('./kernels/'):
+ if op.exists(ctx.get_data('dMRI/kernels.zip')):
+ with zipfile.ZipFile(ctx.get_data('dMRI/kernels.zip'),
+ 'r') as zip_ref:
zip_ref.extractall("./")
with gzip.open(eddy_data_ud, 'rb') as f_in:
@@ -78,10 +81,10 @@ def run(ctx,
# Move files to proper place
for file_n in files:
- old_name = file_n.replace("/NODDI_","/FIT_")
+ old_name = file_n.replace(os.sep + "NODDI_", os.sep + "FIT_")
move(old_name, file_n)
# Delete created folders
for dir_to_delete in [AMICO_dir, NODDI_kernels_dir]:
- if os.path.exists(dir_to_delete):
+ if op.exists(dir_to_delete):
rmtree(dir_to_delete)
diff --git a/bip/pipelines/dMRI_diff/diff_tbss.py b/bip/pipelines/dMRI_diff/diff_tbss.py
index db2dc5b6c9810a6cc32f5ba1b2f0fed35e48ed60..4d0c0830d3e60c710e5b9ea3e1b9f7837783d53f 100755
--- a/bip/pipelines/dMRI_diff/diff_tbss.py
+++ b/bip/pipelines/dMRI_diff/diff_tbss.py
@@ -11,9 +11,11 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
import nibabel as nib
+import numpy as np
from fsl import wrappers
from bip.utils.log_utils import redirect_logging, tempdir, job_name
from pipe_tree import In, Out, Ref
@@ -52,30 +54,33 @@ def run(ctx,
JHUrois_FA: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- TBSS_FA_tmp = tmp_dir + '/TBSS_FA_tmp.nii.gz'
- TBSS_FA_to_MNI_warp_s1 = tmp_dir + '/FA_to_MNI_warp_s1.nii.gz'
- TBSS_FA_to_MNI_warp_s2 = tmp_dir + '/FA_to_MNI_warp_s2.nii.gz'
+ TBSS_FA_tmp = op.join(tmp_dir, 'TBSS_FA_tmp.nii.gz')
+ TBSS_FA_to_MNI_warp_s1 = op.join(tmp_dir, 'FA_to_MNI_warp_s1.nii.gz')
+ TBSS_FA_to_MNI_warp_s2 = op.join(tmp_dir, 'FA_to_MNI_warp_s2.nii.gz')
# Creates links
- # TODO: Do the cool OS.PATH.RELPATH
- if not os.path.exists(TBSS_FA):
- os.symlink(src="../../../" + FA, dst=TBSS_FA)
- if not os.path.exists(TBSS_MNI):
- os.symlink(src=ctx.get_standard('FMRIB58_FA_1mm.nii.gz'), dst=TBSS_MNI)
+ if not op.exists(TBSS_FA):
+ rel_path = op.relpath(FA, TBSS_FA)
+ os.symlink(src=rel_path, dst=TBSS_FA)
+ if not op.exists(TBSS_MNI):
+ os.symlink(src=ctx.get_standard('FMRIB58_FA_1mm.nii.gz'),
+ dst=TBSS_MNI)
FA_img = nib.load(TBSS_FA)
x, y, z = FA_img.header['dim'][1:4]
# erode a little and zero end slices
- wrappers.fslmaths(FA).min(1).ero().roi(1,x,1,y,1,z,0,1).run(TBSS_FA_dir_FA)
+ wrappers.fslmaths(FA).min(1).ero().roi(1,x,1,y,1,z,0,1).\
+ run(TBSS_FA_dir_FA)
# create mask (for use in FLIRT & FNIRT)
wrappers.fslmaths(TBSS_FA_dir_FA).bin().run(TBSS_FA_dir_FA_mask)
#TODO: investigate how to add the -odt=char option
- wrappers.fslmaths(TBSS_FA_dir_FA_mask).dilD(2).sub(1).abs().add(TBSS_FA_dir_FA_mask).run(TBSS_FA_dir_FA_mask)
+ wrappers.fslmaths(TBSS_FA_dir_FA_mask).dilD(2).sub(1).abs().\
+ add(TBSS_FA_dir_FA_mask).run(TBSS_FA_dir_FA_mask, odt="char")
- if not os.path.exists(TBSS_MNI_to_dti_FA_warp_msf):
+ if not op.exists(TBSS_MNI_to_dti_FA_warp_msf):
#New Optimal Registration
wrappers.flirt(ref=TBSS_MNI,
src=TBSS_FA_dir_FA,
@@ -105,7 +110,8 @@ def run(ctx,
# now estimate the mean deformation
- wrappers.fslmaths(TBSS_FA_to_MNI_warp).sqr().Tmean().run(TBSS_FA_tmp)
+ wrappers.fslmaths(TBSS_FA_to_MNI_warp).sqr().Tmean().\
+ run(TBSS_FA_tmp)
mean = wrappers.fslstats(TBSS_FA_tmp).M.run()
median = wrappers.fslstats(TBSS_FA_tmp).P(50).run()
@@ -120,16 +126,20 @@ def run(ctx,
# Create mean FA
skel = ctx.get_standard('FMRIB58_FA-skeleton_1mm.nii.gz')
- wrappers.fslmaths(TBSS_all_FA).bin().mul(TBSS_MNI).bin().run(TBSS_mean_FA_mask)
+ wrappers.fslmaths(TBSS_all_FA).bin().mul(TBSS_MNI).bin().\
+ run(TBSS_mean_FA_mask)
wrappers.fslmaths(TBSS_all_FA).mas(TBSS_mean_FA_mask).run(TBSS_all_FA)
wrappers.fslmaths(TBSS_MNI).mas(TBSS_mean_FA_mask).run(TBSS_mean_FA)
- wrappers.fslmaths(skel).mas(TBSS_mean_FA_mask).run(TBSS_mean_FA_skeleton)
+ wrappers.fslmaths(skel).mas(TBSS_mean_FA_mask).\
+ run(TBSS_mean_FA_skeleton)
# Create Skeleton mask
# TODO: This threshold could be configurable by user
thresh = 2000
- wrappers.fslmaths(TBSS_mean_FA_skeleton).thr(thresh).bin().run(TBSS_mean_FA_skeleton_mask)
- wrappers.fslmaths(TBSS_all_FA).mas(TBSS_mean_FA_skeleton_mask).run(TBSS_all_FA_skeletonised)
+ wrappers.fslmaths(TBSS_mean_FA_skeleton).thr(thresh).bin().\
+ run(TBSS_mean_FA_skeleton_mask)
+ wrappers.fslmaths(TBSS_all_FA).mas(TBSS_mean_FA_skeleton_mask).\
+ run(TBSS_all_FA_skeletonised)
atlas = ctx.get_data('/dMRI/TBSS/JHU-ICBM-labels-1mm.nii.gz')
mean = wrappers.fslstats(TBSS_all_FA_skeletonised, K=atlas).M.run()
@@ -149,14 +159,15 @@ def run(ctx,
d_input = prefix + suffix + ".nii.gz"
- if os.path.exists(d_input):
+ if op.exists(d_input):
d_output = TBSS_prefix + suffix +".nii.gz"
d_output_skel = TBSS_prefix + suffix +"_skeletonised.nii.gz"
d_output_txt = JHUrois_prefix + suffix + '.txt'
wrappers.applywarp(src=d_input, out=d_output, ref=TBSS_MNI,
warp=TBSS_FA_to_MNI_warp, rel=True,
interp='trilinear')
- wrappers.fslmaths(d_output).mas(TBSS_mean_FA_skeleton_mask).run(d_output_skel)
+ wrappers.fslmaths(d_output).\
+ mas(TBSS_mean_FA_skeleton_mask).run(d_output_skel)
mean = wrappers.fslstats( d_output_skel, K=atlas).M.run()
np.savetxt(d_output_txt, mean, fmt="%0.8f")
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
index 89631af1fd229709d7e99af8e9357af70919b483..9036ed1d318fed4f899e51dd16ade459f5fe0f6a 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_post_topup.py
@@ -9,6 +9,7 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os.path as op
import logging
from shutil import copyfile
import numpy as np
@@ -49,13 +50,13 @@ def run(ctx,
fieldmap_iout_mean_ud_inv_warp: Out):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- B0_AP_corr_tmp = tmp_dir + '/B0_AP_corr_tmp.nii.gz'
- B0_PA_corr_tmp = tmp_dir + '/B0_PA_corr_tmp.nii.gz'
- B0_AP_fixed_tmp = tmp_dir + '/B0_AP_fixed_tmp.nii.gz'
- B0_PA_fixed_tmp = tmp_dir + '/B0_PA_fixed_tmp.nii.gz'
- fieldmap_tmp = tmp_dir + '/fieldmap_tmp.nii.gz'
+ B0_AP_corr_tmp = op.join(tmp_dir, 'B0_AP_corr_tmp.nii.gz')
+ B0_PA_corr_tmp = op.join(tmp_dir, 'B0_PA_corr_tmp.nii.gz')
+ B0_AP_fixed_tmp = op.join(tmp_dir, 'B0_AP_fixed_tmp.nii.gz')
+ B0_PA_fixed_tmp = op.join(tmp_dir, 'B0_PA_fixed_tmp.nii.gz')
+ fieldmap_tmp = op.join(tmp_dir, 'fieldmap_tmp.nii.gz')
#Get corrected B=0 for AP and PA and average them avoiding zero values
wrappers.applytopup(imain=B0_AP, datain=acqparams, index=1,
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
index 6dd197045615526fa68e9dbfa326d2eec9dc7b4a..0841b88edc8ac4cd487302f77ba3842e7c3154e8 100755
--- a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup.py
@@ -7,158 +7,20 @@
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
-# pylint: disable=W0613,R0912
+# pylint: disable=W0613,R0912,C0123
#
-import glob
+import os.path as op
import logging
-from shutil import copyfile
-import numpy as np
import nibabel as nib
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging, tempdir, job_name
-from bip.utils.get_b0s import get_b0s
-from bip.utils.get_dwell_time import get_dwell_time
-from bip.utils.read_json_field import read_json_field
from pipe_tree import In, Out, Ref
-
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
+from bip.pipelines.dMRI_fieldmap.fieldmap_pre_topup_fnc import choose_best_B0
+from bip.pipelines.dMRI_fieldmap.fieldmap_pre_topup_fnc import generate_acqparams
log = logging.getLogger(__name__)
-def choose_best_B0(ctx, img, bval, total_B0, indices, tmp, best_index, B0,
- fieldmap_flag, tmp_dir):
-
- blah = tmp_dir + '/blah.nii.gz'
- blah_mat = tmp_dir + '/blah.mat'
-
- b0_threshold=int(np.loadtxt(ctx.get_data('dMRI/b0_threshold.txt')))
-
- bvals = np.loadtxt(bval)
-
- if type(bvals) is not np.ndarray:
- num_vols = 1
- else:
- num_vols = len(np.where(bvals <= b0_threshold)[0])
-
- get_b0s(img, bval, total_B0, indices, num_vols, b0_threshold)
- ind_values = [int(x) for x in np.loadtxt(indices)]
-
- wrappers.fslsplit(total_B0, tmp)
-
- files = glob.glob(tmp + '*')
- files.sort()
-
- N = len(files)
-
- if N == 1:
- with open(best_index, 'wt', encoding="utf-8") as f:
- f.write('0\n')
- copyfile(src=total_B0, dst=B0)
- else:
- scores= np.zeros([N,N])
- for i in range(N):
- for j in range(N):
- if j > i:
- wrappers.flirt(src=files[i], ref=files[j], nosearch=True,
- dof=6, out=blah, omat=blah_mat)
- im1 = nib.load(blah)
- im2 = nib.load(files[j])
- im1f = im1.get_fdata().flatten()
- im2f = im2.get_fdata().flatten()
- corr = np.corrcoef(im1f,im2f)[0,1]
- scores[i,j] = corr
- scores[j,i] = corr
-
- # TODO: Do in one line
- #final_scores = np.zeros(N)
- #for i in range(N):
- # final_scores[i]=np.sum(scores[:,i]) / (N - 1)
- final_scores = np.sum(scores, axis=1) / (N - 1)
-
- best_ind = final_scores.argmax()
- best_score = final_scores[best_ind]
-
- if final_scores[0] > 0.98:
- best_ind = 0
- best_score = final_scores[best_ind]
- if best_score < 0.95:
- with open(fieldmap_flag, 'wt', encoding="utf-8") as f:
- f.write(f'The best score was {best_score}.' +
- 'The subject will probably have problems with this DWI data\n')
- with open(best_index, 'wt', encoding="utf-8") as f:
- f.write(f'{ind_values[best_ind]}\n')
- copyfile(src=files[best_ind], dst=B0)
-
-
-def generate_acqparams(AP, PA, AP_json, PA_json, numAP, numPA, acqparams):
-
- enc_dir_AP = read_json_field(fileName=AP_json,
- fieldName="PhaseEncodingDirection")
- enc_dir_PA = read_json_field(fileName=PA_json,
- fieldName="PhaseEncodingDirection")
-
- # TODO: Write a way to evaluate that they are indeed opposite directions
-
- # Generating the specific strings for the acqparams file for AP
- # according to the Phase Encoding Direction in the AP json file
- if enc_dir_AP == "j-":
- dim_AP = 2
- values_AP = "0 -1 0"
- elif enc_dir_AP == "j":
- dim_AP = 2
- values_AP = "0 1 0"
- elif enc_dir_AP == "i-":
- dim_AP = 1
- values_AP = "-1 0 0"
- elif enc_dir_AP == "i":
- dim_AP = 1
- values_AP = "1 0 0"
- elif enc_dir_AP == "k-":
- dim_AP = 3
- values_AP = "0 0 -1"
- else:
- dim_AP = 3
- values_AP = "0 0 1"
-
- # Generating the specific strings for the acqparams file for PA
- # according to the Phase Encoding Direction in the PA json file
- if enc_dir_PA == "j-":
- #dim_PA = 2
- values_PA = "0 -1 0"
- elif enc_dir_PA == "j":
- #dim_PA = 2
- values_PA = "0 1 0"
- elif enc_dir_PA == "i-":
- #dim_PA = 1
- values_PA = "-1 0 0"
- elif enc_dir_PA == "i":
- #dim_PA = 1
- values_PA = "1 0 0"
- elif enc_dir_PA == "k-":
- #dim_PA = 3
- values_PA = "0 0 -1"
- else:
- #dim_PA = 3
- values_PA = "0 0 1"
-
-
- imAP = nib.load(AP)
- numlines = imAP.header['dim'][dim_AP]
-
- dtiDwell = get_dwell_time(AP, AP_json)
-
- topupValue = (dtiDwell * (numlines -1)) / 1000.0
-
- values_AP = values_AP + " " + str(topupValue) + "\n"
- values_PA = values_PA + " " + str(topupValue) + "\n"
-
- with open(acqparams, 'wt', encoding="utf-8") as f:
- for i in range(numAP):
- f.write(values_AP)
- for i in range(numPA):
- f.write(values_PA)
-
-
def run(ctx,
AP: In,
PA: In,
@@ -182,10 +44,10 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- AP_tmp = tmp_dir + '/AP_tmp_'
- PA_tmp = tmp_dir + '/PA_tmp_'
+ AP_tmp = op.join(tmp_dir, 'AP_tmp_')
+ PA_tmp = op.join(tmp_dir, 'PA_tmp_')
choose_best_B0(ctx, AP, AP_bval, total_B0_AP, AP_indices, AP_tmp,
AP_best_index, B0_AP, AP_fieldmap_flag, tmp_dir)
@@ -204,4 +66,3 @@ def run(ctx,
if (Zslices % 2) != 0:
wrappers.fslroi(B0_AP_PA, B0_AP_PA, 0, -1, 0, -1, 0, Zslices -1)
# TODO: Discuss this with Jesper.
-
diff --git a/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup_fnc.py b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup_fnc.py
new file mode 100755
index 0000000000000000000000000000000000000000..4f378281435e54537c8710acc50c7c6e46040a0c
--- /dev/null
+++ b/bip/pipelines/dMRI_fieldmap/fieldmap_pre_topup_fnc.py
@@ -0,0 +1,153 @@
+#!/usr/bin/env python
+#
+# fieldmap_pre_topup.py - Sub-pipeline with the fieldmap processing before topup
+#
+# 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
+# pylint: disable=W0613,R0912,W0612
+#
+
+import os.path as op
+import glob
+import logging
+from shutil import copyfile
+import numpy as np
+import nibabel as nib
+from fsl import wrappers
+from bip.utils.get_b0s import get_b0s
+from bip.utils.get_dwell_time import get_dwell_time
+from bip.utils.read_json_field import read_json_field
+
+log = logging.getLogger(__name__)
+
+def choose_best_B0(ctx, img, bval, total_B0, indices, tmp, best_index, B0,
+ fieldmap_flag, tmp_dir):
+
+ blah = op.join(tmp_dir, 'blah.nii.gz')
+ blah_mat = op.join(tmp_dir, 'blah.mat')
+
+ b0_threshold=int(np.loadtxt(ctx.get_data('dMRI/b0_threshold.txt')))
+
+ bvals = np.loadtxt(bval)
+
+ if type(bvals) is not np.ndarray:
+ num_vols = 1
+ else:
+ num_vols = len(np.where(bvals <= b0_threshold)[0])
+
+ get_b0s(img, bval, total_B0, indices, num_vols, b0_threshold)
+ ind_values = [int(x) for x in np.loadtxt(indices)]
+
+ wrappers.fslsplit(total_B0, tmp)
+
+ files = glob.glob(tmp + '*')
+ files.sort()
+
+ N = len(files)
+
+ if N == 1:
+ with open(best_index, 'wt', encoding="utf-8") as f:
+ f.write('0\n')
+ copyfile(src=total_B0, dst=B0)
+ else:
+ scores= np.zeros([N,N])
+ for i in range(N):
+ for j in range(N):
+ if j > i:
+ wrappers.flirt(src=files[i], ref=files[j], nosearch=True,
+ dof=6, out=blah, omat=blah_mat)
+ im1 = nib.load(blah)
+ im2 = nib.load(files[j])
+ im1f = im1.get_fdata().flatten()
+ im2f = im2.get_fdata().flatten()
+ corr = np.corrcoef(im1f,im2f)[0,1]
+ scores[i,j] = corr
+ scores[j,i] = corr
+
+ final_scores = np.sum(scores, axis=1) / (N - 1)
+
+ best_ind = final_scores.argmax()
+ best_score = final_scores[best_ind]
+
+ if final_scores[0] > 0.98:
+ best_ind = 0
+ best_score = final_scores[best_ind]
+ if best_score < 0.95:
+ with open(fieldmap_flag, 'wt', encoding="utf-8") as f:
+ f.write(f'The best score was {best_score}.' +
+ 'The subject will probably have problems with this DWI data\n')
+ with open(best_index, 'wt', encoding="utf-8") as f:
+ f.write(f'{ind_values[best_ind]}\n')
+ copyfile(src=files[best_ind], dst=B0)
+
+
+def generate_acqparams(AP, PA, AP_json, PA_json, numAP, numPA, acqparams):
+
+ enc_dir_AP = read_json_field(fileName=AP_json,
+ fieldName="PhaseEncodingDirection")
+ enc_dir_PA = read_json_field(fileName=PA_json,
+ fieldName="PhaseEncodingDirection")
+
+ # TODO: Write a way to evaluate that they are indeed opposite directions
+
+ # Generating the specific strings for the acqparams file for AP
+ # according to the Phase Encoding Direction in the AP json file
+ if enc_dir_AP == "j-":
+ dim_AP = 2
+ values_AP = "0 -1 0"
+ elif enc_dir_AP == "j":
+ dim_AP = 2
+ values_AP = "0 1 0"
+ elif enc_dir_AP == "i-":
+ dim_AP = 1
+ values_AP = "-1 0 0"
+ elif enc_dir_AP == "i":
+ dim_AP = 1
+ values_AP = "1 0 0"
+ elif enc_dir_AP == "k-":
+ dim_AP = 3
+ values_AP = "0 0 -1"
+ else:
+ dim_AP = 3
+ values_AP = "0 0 1"
+
+ # Generating the specific strings for the acqparams file for PA
+ # according to the Phase Encoding Direction in the PA json file
+ if enc_dir_PA == "j-":
+ #dim_PA = 2
+ values_PA = "0 -1 0"
+ elif enc_dir_PA == "j":
+ #dim_PA = 2
+ values_PA = "0 1 0"
+ elif enc_dir_PA == "i-":
+ #dim_PA = 1
+ values_PA = "-1 0 0"
+ elif enc_dir_PA == "i":
+ #dim_PA = 1
+ values_PA = "1 0 0"
+ elif enc_dir_PA == "k-":
+ #dim_PA = 3
+ values_PA = "0 0 -1"
+ else:
+ #dim_PA = 3
+ values_PA = "0 0 1"
+
+
+ imAP = nib.load(AP)
+ numlines = imAP.header['dim'][dim_AP]
+
+ dtiDwell = get_dwell_time(AP, AP_json)
+
+ topupValue = (dtiDwell * (numlines -1)) / 1000.0
+
+ values_AP = values_AP + " " + str(topupValue) + "\n"
+ values_PA = values_PA + " " + str(topupValue) + "\n"
+
+ with open(acqparams, 'wt', encoding="utf-8") as f:
+ for i in range(numAP):
+ f.write(values_AP)
+ for i in range(numPA):
+ f.write(values_PA)
diff --git a/bip/pipelines/fMRI_rest/rfMRI_fix.py b/bip/pipelines/fMRI_rest/rfMRI_fix.py
index abe65fc79647dd7b09ae2b5a51d453c6daa1a4f8..781af126f17a56ee3c80bb40d4c38d98d78bf013 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_fix.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_fix.py
@@ -10,6 +10,7 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
@@ -42,22 +43,22 @@ def run(ctx,
with redirect_logging('rfMRI_fix', outdir=logs_dir):
# Generate files needed to extract features
- if not os.path.exists(rfMRI_highres_pveseg):
+ if not op.exists(rfMRI_highres_pveseg):
copyfile(T1_fast_pveseg, rfMRI_highres_pveseg)
- if not os.path.exists(rfMRI_standard2example_func_warp):
+ if not op.exists(rfMRI_standard2example_func_warp):
wrappers.invwarp(ref=rfMRI_example_func,
warp=rfMRI_example_func2standard_warp,
out=rfMRI_standard2example_func_warp)
# FIX: Extract features for subject
- if not os.path.exists(fix_features):
+ if not op.exists(fix_features):
d = extract.FixData.from_melodic_dir(rfMRI_ica, fixdir = fix_dir)
f = extract.extract_features(data=d,
features=legacy.LEGACY_FEATURE_EXTRACTORS)
- io.save_features(os.path.join(fix_dir, 'features'), f)
+ io.save_features(op.join(fix_dir, 'features'), f)
else:
- f = io.read_features(os.path.join(fix_dir, 'features'))
+ f = io.read_features(op.join(fix_dir, 'features'))
# FIX: Classify components for subject
clf = io.load_model(ctx.get_data('/fix/UKBB_model_2.pyfix_model'))
@@ -85,7 +86,7 @@ def run(ctx,
# Create this directory in case it does not exist. This may
# happen due to the overwrite function issue in Melodic
- if not os.path.exists(rfMRI_reg_standard_dir):
+ if not op.exists(rfMRI_reg_standard_dir):
os.mkdir(rfMRI_reg_standard_dir)
# Generate the data in standard space
diff --git a/bip/pipelines/fMRI_rest/rfMRI_melodic.py b/bip/pipelines/fMRI_rest/rfMRI_melodic.py
index 8469ae8b22afca718af4d52b5f00beb705105848..33ae209540f1dd0f9137a6e56d067dfa13e52d21 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_melodic.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_melodic.py
@@ -12,6 +12,7 @@
#
import os
+import os.path as op
import shutil
import logging
from fsl import wrappers
@@ -44,7 +45,7 @@ def run(ctx,
name_dir_alt[-2] = name_dir_alt[-2] + "+"
name_dir_alt = ".".join(name_dir_alt)
- if os.path.exists(name_dir_alt):
- if os.path.exists(rfMRI_ica):
+ if op.exists(name_dir_alt):
+ if op.exists(rfMRI_ica):
shutil.rmtree(rfMRI_ica)
os.rename(name_dir_alt, rfMRI_ica)
diff --git a/bip/pipelines/fMRI_rest/rfMRI_netmats.py b/bip/pipelines/fMRI_rest/rfMRI_netmats.py
index c110d3d82b5fbd22c88be835b83e805668be43c7..651b83ede834c0a201f7c8cd31264c034cfaf5c6 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_netmats.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_netmats.py
@@ -10,6 +10,7 @@
#
import os
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref, Var
@@ -39,7 +40,7 @@ def run(ctx,
# Create this directory in case it does not exist. This may
# happen due to the overwrite function issue in Melodic
- if not os.path.exists(netmats_dir):
+ if not op.exists(netmats_dir):
os.mkdir(netmats_dir)
diff --git a/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py b/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py
index dcc4d5e325fb213cf6b30f699694ef5fa3570d11..106575f1fb8281cb4fbcdc4581c5292f5701541b 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_netmats_fnc.py
@@ -10,6 +10,7 @@
# pylint: disable=E1130
#
+import os.path as op
import numpy as np
import nibabel as nib
@@ -79,7 +80,7 @@ def nets_netmats(ts, do_rtoz, method, arg_method=None):
elif method.lower() in ['ridgep']:
grot=np.cov(grot, rowvar=False)
- grot=grot/np.sqrt(np.nanmean(np.diag(grot) * np.diag(grot)))
+ grot=grot / np.sqrt(np.nanmean(np.diag(grot) * np.diag(grot)))
if not arg_method:
rho=0.1
else:
diff --git a/bip/pipelines/fMRI_rest/rfMRI_prepare.py b/bip/pipelines/fMRI_rest/rfMRI_prepare.py
index 8af1d403bf28f17c91b32d15e2d551ddc796ab29..d469ff45355f761a03ae83294e9a4f638b3632ee 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_prepare.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_prepare.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
import nibabel as nib
@@ -48,20 +49,23 @@ def run(ctx,
# Creates links
# TODO: These links ARE hard-coded. This may cause future problems.
- if not os.path.exists(rfMRI_T1):
- os.symlink(src="../../T1/T1.nii.gz",
- dst=rfMRI_T1)
- if not os.path.exists(rfMRI_T1_brain):
- os.symlink(src="../../T1/T1_brain.nii.gz",
- dst=rfMRI_T1_brain)
- if not os.path.exists(rfMRI_T1_brain2MNI152_T1_2mm_brain_warp):
- os.symlink(src="../../T1/transforms/T1_to_MNI_warp.nii.gz",
- dst=rfMRI_T1_brain2MNI152_T1_2mm_brain_warp)
- if not os.path.exists(rfMRI_T1_brain2MNI152_T1_2mm_brain_mat):
- os.symlink(src="../../T1/transforms/T1_to_MNI_linear.mat",
- dst=rfMRI_T1_brain2MNI152_T1_2mm_brain_mat)
-
- wrappers.fslmaths(T1_fast_pve_2).thr(0.5).bin().run(rfMRI_T1_brain_wmseg)
+ if not op.exists(rfMRI_T1):
+ rel_path = op.relpath(T1, rfMRI_T1)
+ os.symlink(src=rel_path, dst=rfMRI_T1)
+ if not op.exists(rfMRI_T1_brain):
+ rel_path = op.relpath(T1_brain, rfMRI_T1_brain)
+ os.symlink(src=rel_path, dst=rfMRI_T1_brain)
+ if not op.exists(rfMRI_T1_brain2MNI152_T1_2mm_brain_warp):
+ rel_path = op.relpath(T1_to_MNI_warp,
+ rfMRI_T1_brain2MNI152_T1_2mm_brain_warp)
+ os.symlink(src=rel_path,dst=rfMRI_T1_brain2MNI152_T1_2mm_brain_warp)
+ if not op.exists(rfMRI_T1_brain2MNI152_T1_2mm_brain_mat):
+ rel_path = op.relpath(T1_to_MNI_linear_mat,
+ rfMRI_T1_brain2MNI152_T1_2mm_brain_mat)
+ os.symlink(src=rel_path, dst=rfMRI_T1_brain2MNI152_T1_2mm_brain_mat)
+
+ wrappers.fslmaths(T1_fast_pve_2).thr(0.5).bin().\
+ run(rfMRI_T1_brain_wmseg)
# Generation of FSF file
copyfile(src=ctx.get_data('fMRI_fsf/design_ICA_nonSmoothed.fsf'),
@@ -98,16 +102,31 @@ def run(ctx,
copyfile(src=rfMRI_SBREF, dst=rfMRI_SBREF_ud)
with open(rfMRI_fsf, 'a', encoding="utf-8") as f:
- f.write('set fmri(regstandard) "' + ctx.FSLDIR + \
- '/data/standard/MNI152_T1_2mm_brain"\n')
- f.write('set fmri(outputdir) "' + os.getcwd() + "/" + rfMRI_ica + '"\n')
- f.write('set feat_files(1) "' + os.getcwd() + "/" + rfMRI + '"\n')
- f.write('set alt_ex_func(1) "' + os.getcwd() + "/" + rfMRI_SBREF + '"\n')
- f.write('set unwarp_files(1) "' + os.getcwd() + "/" + fieldmap_fout_to_T1_brain_rad + '"\n')
- f.write('set unwarp_files_mag(1) "' + os.getcwd() + "/" + rfMRI_T1_brain + '"\n')
- f.write('set highres_files(1) "' + os.getcwd() + "/" + rfMRI_T1_brain + '"\n')
+ file_name = ctx.get_standard("MNI152_T1_2mm_brain")
+ f.write('set fmri(regstandard) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), rfMRI_ica)
+ f.write('set fmri(outputdir) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), rfMRI)
+ f.write('set feat_files(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), rfMRI_SBREF)
+ f.write('set alt_ex_func(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), fieldmap_fout_to_T1_brain_rad)
+ f.write('set unwarp_files(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), rfMRI_T1_brain)
+ f.write('set unwarp_files_mag(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), rfMRI_T1_brain)
+ f.write('set highres_files(1) "' + file_name + '"\n')
+
if ctx.gdc != '':
- f.write('set fmri(gdc) "' + os.getcwd() + "/" + rfMRI_SBREF_ud_warp + '"\n')
+ file_name = op.join(os.getcwd(), rfMRI_SBREF_ud_warp)
+ f.write('set fmri(gdc) "' + file_name + '"\n')
+
f.write('set fmri(tr) ' + str(fmriTR) + '\n')
f.write('set fmri(npts) ' + str(fmriNumVol) + '\n')
f.write('set fmri(dwell) ' + str(fmriDwell) + '\n')
diff --git a/bip/pipelines/fMRI_task/tfMRI_feat.py b/bip/pipelines/fMRI_task/tfMRI_feat.py
index 6b275525175a3f2a64c06595ddccd59ffa3a75c2..318a710827a031d7a8b5b4f5979556d5b8aec119 100755
--- a/bip/pipelines/fMRI_task/tfMRI_feat.py
+++ b/bip/pipelines/fMRI_task/tfMRI_feat.py
@@ -10,6 +10,9 @@
# pylint: disable=W0613
#
+import os
+import os.path as op
+import shutil
import logging
from fsl import wrappers
from bip.utils.log_utils import redirect_logging
@@ -47,7 +50,7 @@ def run(ctx,
name_dir_alt[-2] = name_dir_alt[-2] + "+"
name_dir_alt = ".".join(name_dir_alt)
- if os.path.exists(name_dir_alt):
- if os.path.exists(tfMRI_feat):
+ if op.exists(name_dir_alt):
+ if op.exists(tfMRI_feat):
shutil.rmtree(tfMRI_feat)
os.rename(name_dir_alt, tfMRI_feat)
diff --git a/bip/pipelines/fMRI_task/tfMRI_prepare.py b/bip/pipelines/fMRI_task/tfMRI_prepare.py
index 06bc292f207f208142074a436bb2c35fd8fcbeb4..c309b45ea5513239d50f2d0236f3cdd1ba16f1ee 100755
--- a/bip/pipelines/fMRI_task/tfMRI_prepare.py
+++ b/bip/pipelines/fMRI_task/tfMRI_prepare.py
@@ -11,6 +11,7 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
import nibabel as nib
@@ -48,20 +49,23 @@ def run(ctx,
# Creates links
# TODO: These links ARE hard-coded. This may cause future problems.
- if not os.path.exists(tfMRI_T1):
- os.symlink(src="../../T1/T1.nii.gz",
- dst=tfMRI_T1)
- if not os.path.exists(tfMRI_T1_brain):
- os.symlink(src="../../T1/T1_brain.nii.gz",
- dst=tfMRI_T1_brain)
- if not os.path.exists(tfMRI_T1_brain2MNI152_T1_2mm_brain_warp):
- os.symlink(src="../../T1/transforms/T1_to_MNI_warp.nii.gz",
- dst=tfMRI_T1_brain2MNI152_T1_2mm_brain_warp)
- if not os.path.exists(tfMRI_T1_brain2MNI152_T1_2mm_brain_mat):
- os.symlink(src="../../T1/transforms/T1_to_MNI_linear.mat",
- dst=tfMRI_T1_brain2MNI152_T1_2mm_brain_mat)
-
- wrappers.fslmaths(T1_fast_pve_2).thr(0.5).bin().run(tfMRI_T1_brain_wmseg)
+ if not op.exists(tfMRI_T1):
+ rel_path = op.relpath(T1, tfMRI_T1)
+ os.symlink(src=rel_path, dst=tfMRI_T1)
+ if not op.exists(tfMRI_T1_brain):
+ rel_path = op.relpath(T1_brain, tfMRI_T1_brain)
+ os.symlink(src=rel_path, dst=tfMRI_T1_brain)
+ if not op.exists(tfMRI_T1_brain2MNI152_T1_2mm_brain_warp):
+ rel_path = op.relpath(T1_to_MNI_warp,
+ tfMRI_T1_brain2MNI152_T1_2mm_brain_warp)
+ os.symlink(src=rel_path,dst=tfMRI_T1_brain2MNI152_T1_2mm_brain_warp)
+ if not op.exists(tfMRI_T1_brain2MNI152_T1_2mm_brain_mat):
+ rel_path = op.relpath(T1_to_MNI_linear_mat,
+ tfMRI_T1_brain2MNI152_T1_2mm_brain_mat)
+ os.symlink(src=rel_path,dst=tfMRI_T1_brain2MNI152_T1_2mm_brain_mat)
+
+ wrappers.fslmaths(T1_fast_pve_2).thr(0.5).bin().\
+ run(tfMRI_T1_brain_wmseg)
# Generation of FSF file
copyfile(src=ctx.get_data('fMRI_fsf/design_TASK.fsf'), dst=tfMRI_fsf)
@@ -97,18 +101,37 @@ def run(ctx,
copyfile(src=tfMRI_SBREF, dst=tfMRI_SBREF_ud)
with open(tfMRI_fsf, 'a', encoding="utf-8") as f:
- f.write('set fmri(regstandard) "' + ctx.FSLDIR + \
- '/data/standard/MNI152_T1_2mm_brain"\n')
- f.write('set fmri(custom1) "' + ctx.get_data('fMRI_fsf/designS.txt') + '"\n')
- f.write('set fmri(custom2) "' + ctx.get_data('fMRI_fsf/designF.txt') + '"\n')
- f.write('set fmri(outputdir) "' + os.getcwd() + "/" + tfMRI_feat + '"\n')
- f.write('set feat_files(1) "' + os.getcwd() + "/" + tfMRI + '"\n')
- f.write('set alt_ex_func(1) "' + os.getcwd() + "/" + tfMRI_SBREF + '"\n')
- f.write('set unwarp_files(1) "' + os.getcwd() + "/" + fieldmap_fout_to_T1_brain_rad + '"\n')
- f.write('set unwarp_files_mag(1) "' + os.getcwd() + "/" + tfMRI_T1_brain + '"\n')
- f.write('set highres_files(1) "' + os.getcwd() + "/" + tfMRI_T1_brain + '"\n')
+ file_name = ctx.get_standard("MNI152_T1_2mm_brain")
+ f.write('set fmri(regstandard) "' + file_name + '"\n')
+
+ file_name = ctx.get_data('fMRI_fsf/designS.txt')
+ f.write('set fmri(custom1) "' + file_name + '"\n')
+
+ file_name = ctx.get_data('fMRI_fsf/designF.txt')
+ f.write('set fmri(custom2) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), tfMRI_feat)
+ f.write('set fmri(outputdir) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), tfMRI)
+ f.write('set feat_files(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), tfMRI_SBREF)
+ f.write('set alt_ex_func(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), fieldmap_fout_to_T1_brain_rad)
+ f.write('set unwarp_files(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), tfMRI_T1_brain)
+ f.write('set unwarp_files_mag(1) "' + file_name + '"\n')
+
+ file_name = op.join(os.getcwd(), tfMRI_T1_brain)
+ f.write('set highres_files(1) "' + file_name + '"\n')
+
if ctx.gdc != '':
- f.write('set fmri(gdc) "' + os.getcwd() + "/" + tfMRI_SBREF_ud_warp + '"\n')
+ file_name = op.join(os.getcwd(), tfMRI_SBREF_ud_warp)
+ f.write('set fmri(gdc) "' + file_name + '"\n')
+
f.write('set fmri(tr) ' + str(fmriTR) + '\n')
f.write('set fmri(npts) ' + str(fmriNumVol) + '\n')
f.write('set fmri(dwell) ' + str(fmriDwell) + '\n')
diff --git a/bip/pipelines/struct_FS/FS_get_IDPs.py b/bip/pipelines/struct_FS/FS_get_IDPs.py
index 3dee9ab76100572fc21b351892586b1b76247682..f1f37129deca8983ad7a4c1902ffc27186cbdef6 100755
--- a/bip/pipelines/struct_FS/FS_get_IDPs.py
+++ b/bip/pipelines/struct_FS/FS_get_IDPs.py
@@ -11,9 +11,8 @@
#
import os
-import sys
+import os.path as op
import logging
-import argparse
from pipe_tree import In, Out, Ref
from bip.pipelines.struct_FS.FS_get_IDPs_fnc import bb_FS_get_IDPs
from bip.utils.log_utils import redirect_logging, job_name
@@ -28,6 +27,6 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- env = dict(os.environ, SUBJECTS_DIR=os.getcwd() + "/" + ctx.subject)
+ env = dict(os.environ, SUBJECTS_DIR=op.join(os.getcwd(), ctx.subject))
bb_FS_get_IDPs(ctx, env)
diff --git a/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py b/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py
index 3a14ccf4e66f4078c34c6066b3c94741aa8741c8..44fef49b535ea503a9676a75ba515fe14cd8b42e 100755
--- a/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py
+++ b/bip/pipelines/struct_FS/FS_get_IDPs_fnc.py
@@ -11,24 +11,12 @@
#
import os
-import sys
+import os.path as op
import logging
-import argparse
-from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging, run_command
+from bip.utils.log_utils import run_command
log = logging.getLogger(__name__)
-class MyParser(argparse.ArgumentParser):
- def error(self, message):
- sys.stderr.write(f'error: {message}\n')
- self.print_help()
- sys.exit(2)
-
-class Usage(Exception):
- def __init__(self, msg):
- self.msg = msg
-
def check_and_create_dir(dirName):
try:
os.stat(dirName)
@@ -47,49 +35,51 @@ def read_file(fileName):
def generate_FS_IDP_files(SUBJECTS_DIR, subject_ID, subject, dataDir,
headersDir, ctx, env):
- statsDir = SUBJECTS_DIR + '/' + subject_ID + '/stats/'
+ statsDir = op.join(SUBJECTS_DIR, subject_ID, 'stats') + os.sep
#TODO: Include a pre-requisite that python2.7 must be availble in the system
- if os.path.isfile(statsDir + 'aseg.stats'):
+ if op.isfile(statsDir + 'aseg.stats'):
run_command(log, 'asegstats2table '+
' -m volume --all-segs --tablefile ' + dataDir + 'aseg_1.txt ' +
- ' --subjects ' + subject_ID + ' --skip', env)
+ ' --subjects ' + subject_ID + ' --skip', env=env)
run_command(log, 'asegstats2table '+
' -m mean --all-segs --tablefile ' + dataDir +
- 'aseg_intensity.txt ' +' --subjects ' + subject_ID + ' --skip', env)
+ 'aseg_intensity.txt ' +' --subjects ' + subject_ID + ' --skip',
+ env=env)
- if os.path.isfile(statsDir + 'lh.w-g.pct.stats'):
+ if op.isfile(statsDir + 'lh.w-g.pct.stats'):
run_command(log, 'asegstats2table ' +
' -m mean --all-segs --stats=lh.w-g.pct.stats ' +
' --tablefile ' + dataDir + 'wg_lh_mean.txt ' +
- ' --subjects ' + subject_ID + ' --skip', env)
+ ' --subjects ' + subject_ID + ' --skip', env=env)
- if os.path.isfile(statsDir + 'rh.w-g.pct.stats'):
+ if op.isfile(statsDir + 'rh.w-g.pct.stats'):
run_command(log, 'asegstats2table ' +
' -m mean --all-segs --stats=rh.w-g.pct.stats ' +
' --tablefile ' + dataDir + 'wg_rh_mean.txt ' +
- ' --subjects ' + subject_ID + ' --skip', env)
+ ' --subjects ' + subject_ID + ' --skip', env=env)
for hemi in ["lh", "rh"]:
for value in ["volume", "area", "thickness"]:
for atlas in ["BA_exvivo", "aparc.DKTatlas", "aparc.a2009s",
"aparc"]:
outFileName = dataDir + atlas + '_' + hemi + '_' + value + '.txt'
- if os.path.isfile(statsDir + hemi + "." + atlas + '.stats'):
+ if op.isfile(statsDir + hemi + "." + atlas + '.stats'):
run_command(log, 'aparcstats2table '+
' -m ' + value + ' --hemi=' + hemi +
' --tablefile ' + outFileName +
- ' --subjects ' + subject_ID + ' --skip -p ' + atlas,env)
+ ' --subjects ' + subject_ID + ' --skip -p ' + atlas,
+ env=env)
atlas="aparc.pial"
value="area"
for hemi in ["lh", "rh"]:
outFileName = dataDir + atlas + '_' + hemi + '_' + value + '.txt'
- if os.path.isfile(statsDir + hemi + '.aparc.pial.stats'):
+ if op.isfile(statsDir + hemi + '.aparc.pial.stats'):
run_command(log, 'aparcstats2table '+
' -m ' + value + ' --hemi=' + hemi +
' --tablefile ' + outFileName +
- ' --subjects ' + subject_ID + ' --skip -p ' + atlas, env)
+ ' --subjects ' + subject_ID + ' --skip -p ' + atlas, env=env)
with open(ctx.get_data('FS/FS_initial_files.txt'), encoding="utf-8") as f:
files_generated = [x.replace('\n','').split(" ") for x in f.readlines()]
@@ -97,7 +87,7 @@ def generate_FS_IDP_files(SUBJECTS_DIR, subject_ID, subject, dataDir,
data_dict={}
for file_generated in files_generated:
- if os.path.isfile(dataDir + file_generated[0] + '.txt'):
+ if op.isfile(dataDir + file_generated[0] + '.txt'):
data = read_file(dataDir + file_generated[0] + '.txt')
else:
data = read_file(ctx.get_data('FS/FS_data_ex/' +
@@ -114,17 +104,17 @@ def check_consistency(data_dict, SUBJECTS_DIR, ctx):
for file_generated in data_dict.keys():
if len(data_dict[file_generated])>2:
- print("Error in " + file_generated + ': File has more than 2 lines')
save_data_NaNs(SUBJECTS_DIR, ctx)
- sys.exit(-1)
+ raise Exception("Error in " + file_generated + \
+ ': File has more than 2 lines')
len0=len(data_dict[file_generated][0])
len1=len(data_dict[file_generated][1])
if len0 != len1:
- print("Error in " + file_generated + ': Inconsistent # of features')
save_data_NaNs(SUBJECTS_DIR, ctx)
- sys.exit(-1)
+ raise Exception("Error in " + file_generated + \
+ ': Inconsistent # of features')
def fix_aseg_data(data_dict, subjectDir):
@@ -148,7 +138,8 @@ def fix_aseg_data(data_dict, subjectDir):
# For some reason, the VentricleChoroidVol is not caught by asegstats2table
try:
- with open(subjectDir + '/stats/aseg.stats', 'r', encoding="utf-8") as f:
+ file_name = op.join(subjectDir, 'stats' , 'aseg.stats')
+ with open(, 'r', encoding="utf-8") as f:
val=[x.split(',')[3].strip() for x in f.readlines() if 'VentricleChoroidVol' in x]
except:
val=["NaN"]
@@ -207,7 +198,7 @@ def gen_aparc_special(data_dict, subjectDir):
def bool_FLAIR(data_dict, subjectDir):
- if os.path.isfile(subjectDir + '/mri/FLAIR.mgz'):
+ if op.isfile(subjectDir + '/mri/FLAIR.mgz'):
data_dict['FLAIR'] = [['Use-T2-FLAIR-for-FreeSurfer'],['1']]
else:
data_dict['FLAIR'] = [['Use-T2-FLAIR-for-FreeSurfer'],['0']]
@@ -233,7 +224,7 @@ def gen_subsegmentation(data_dict, subjectDir, subject, ctx):
data_dict[struct] = [[],[]]
for fil in struct_data[struct][0]:
final_fil = subjectDir + '/FreeSurfer/mri/' + fil
- if os.path.isfile(final_fil):
+ if op.isfile(final_fil):
with open(final_fil, 'r',encoding="utf-8") as f:
for lin in f.readlines():
lin = lin.replace('\n','').split(' ')
@@ -518,9 +509,8 @@ def bb_FS_get_IDPs(ctx, env):
headersDir = subjectDir + '/headers/'
#TODO: Raise an exception
- if not os.path.isdir(subjectDir):
- print("Error: FreeSurfer has not been run on this subject")
- sys.exit(-1)
+ if not op.isdir(subjectDir):
+ raise Exception("Error: FreeSurfer has not been run on this subject")
check_and_create_dir(dataDir)
check_and_create_dir(headersDir)
@@ -537,16 +527,3 @@ def bb_FS_get_IDPs(ctx, env):
check_consistency(data_dict, subjectDir, ctx)
save_data(data_dict, subjectDir, ctx)
-
-
-def run(ctx,
- ThalamicNuclei: In,
- rh_entorhinal_exvivo_label: In,
- logs_dir: Ref,
- FS_IDPs: Out):
-
- with redirect_logging('FS_get_IDPs', outdir=logs_dir):
-
- env = dict(os.environ, SUBJECTS_DIR=os.getcwd() + "/" + ctx.subject)
-
- bb_FS_get_IDPs(ctx, env)
diff --git a/bip/pipelines/struct_FS/FS_proc.py b/bip/pipelines/struct_FS/FS_proc.py
index 7e3f834b4ea26bccf3a485328ff1e0a55641ff25..3b4f14e922c2792bcd884ae309249e72ccf1dc84 100755
--- a/bip/pipelines/struct_FS/FS_proc.py
+++ b/bip/pipelines/struct_FS/FS_proc.py
@@ -11,10 +11,11 @@
#
import os
+import os.path as op
import shutil
import logging
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging, run_command
+from bip.utils.log_utils import redirect_logging, run_command, job_name
log = logging.getLogger(__name__)
@@ -29,24 +30,24 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
# We need to delete the folder because otherwise, FreeSurfer complains
- if os.path.exists(FreeSurfer_dir):
+ if op.exists(FreeSurfer_dir):
shutil.rmtree(FreeSurfer_dir)
#TODO: SUBJECTS_DIR can be an argument of freesurfer instead of this craps
- env = dict(os.environ, SUBJECTS_DIR=os.getcwd() + "/" + ctx.subject)
+ env = dict(os.environ, SUBJECTS_DIR=op.join(os.getcwd(), ctx.subject))
- T1_path = os.getcwd() + "/" + T1_unbiased
- T2_path = os.getcwd() + "/" + T2_FLAIR_unbiased
+ T1_path = op.join(os.getcwd(), T1_unbiased)
+ T2_path = op.join(os.getcwd(), T2_FLAIR_unbiased)
cmd = 'recon-all -all -s FreeSurfer -i ' + T1_path
#TODO: Do this for all cases of os.path.exits (all optional things)
- if T2_FLAIR_unbiased is not None and os.path.exists(T2_FLAIR_unbiased):
+ if T2_FLAIR_unbiased is not None and op.exists(T2_FLAIR_unbiased):
cmd += " -FLAIR " + T2_path + " -FLAIRpial"
try:
output = run_command(log, cmd, env=env)
log.info(output)
finally:
- if os.path.exists(fsaverage):
+ if op.exists(fsaverage):
os.unlink(fsaverage)
diff --git a/bip/pipelines/struct_FS/FS_segm.py b/bip/pipelines/struct_FS/FS_segm.py
index 0e646224685d391394ca4f0749992b9200356673..7f7fde392eb816754078a9adbba8e184f4b6ebb1 100755
--- a/bip/pipelines/struct_FS/FS_segm.py
+++ b/bip/pipelines/struct_FS/FS_segm.py
@@ -11,9 +11,10 @@
#
import os
+import os.path as op
import logging
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging, run_command
+from bip.utils.log_utils import redirect_logging, run_command, job_name
log = logging.getLogger(__name__)
@@ -27,18 +28,18 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
- env = dict(os.environ, SUBJECTS_DIR=os.getcwd() + "/" + ctx.subject)
+ env = dict(os.environ, SUBJECTS_DIR=op.join(os.getcwd(), ctx.subject))
- output1 = run_command(log, 'segmentThalamicNuclei.sh FreeSurfer', env)
+ output1 = run_command(log, 'segmentThalamicNuclei.sh FreeSurfer', env=env)
log.info(output1)
- output2 = run_command(log, 'segmentBS.sh FreeSurfer', env)
+ output2 = run_command(log, 'segmentBS.sh FreeSurfer', env=env)
log.info(output2)
- if os.path.exists(T2_FLAIR_unbiased):
+ if op.exists(T2_FLAIR_unbiased):
output3 = run_command(log,
'segmentHA_T2.sh FreeSurfer ' + FreSurfer_FLAIR + ' AN 1',
- env)
+ env=env)
else:
- output3 = run_command(log, 'segmentHA_T1.sh FreeSurfer', env)
+ output3 = run_command(log, 'segmentHA_T1.sh FreeSurfer', env=env)
log.info(output3)
diff --git a/bip/pipelines/struct_T1/T1_QC_CNR_corners.py b/bip/pipelines/struct_T1/T1_QC_CNR_corners.py
index dd3d960c1f8c464f42f9534c57fc54bfad7ba486..40c686e20e91b6cb42cd3bb2dc7e416fba888352 100755
--- a/bip/pipelines/struct_T1/T1_QC_CNR_corners.py
+++ b/bip/pipelines/struct_T1/T1_QC_CNR_corners.py
@@ -10,10 +10,11 @@
# pylint: disable=W0613
#
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
log = logging.getLogger(__name__)
@@ -31,16 +32,16 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
-
- roi_1_1 = tmp_dir + '/roi_1_1.nii.gz'
- roi_1_245 = tmp_dir + '/roi_1_245.nii.gz'
- roi_197_1 = tmp_dir + '/roi_197_1.nii.gz'
- roi_197_245 = tmp_dir + '/roi_197_245.nii.gz'
- roi_x_1 = tmp_dir + '/roi_x_1.nii.gz'
- roi_x_245 = tmp_dir + '/roi_x_245.nii.gz'
- roi_lower = tmp_dir + '/roi_lower.nii.gz'
- roi_upper = tmp_dir + '/roi_upper.nii.gz'
+ tempdir(op.join(tmp_dir, job_name(run))):
+
+ roi_1_1 = op.join(tmp_dir, 'roi_1_1.nii.gz')
+ roi_1_245 = op.join(tmp_dir, 'roi_1_245.nii.gz')
+ roi_197_1 = op.join(tmp_dir, 'roi_197_1.nii.gz')
+ roi_197_245 = op.join(tmp_dir, 'roi_197_245.nii.gz')
+ roi_x_1 = op.join(tmp_dir, 'roi_x_1.nii.gz')
+ roi_x_245 = op.join(tmp_dir, 'roi_x_245.nii.gz')
+ roi_lower = op.join(tmp_dir, 'roi_lower.nii.gz')
+ roi_upper = op.join(tmp_dir, 'roi_upper.nii.gz')
in_files = [T1_orig, T1_notNorm]
diff --git a/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py b/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
index fac3844700b7552653e4761bc4592de8421802af..3637366a7b3fecc7395fecb9ffcf15ef51533996 100755
--- a/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
+++ b/bip/pipelines/struct_T1/T1_QC_CNR_eyes.py
@@ -10,13 +10,13 @@
# pylint: disable=W0613
#
-
import os
+import os.path as op
import logging
import nibabel as nib
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
log = logging.getLogger(__name__)
@@ -41,15 +41,15 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- T1_brain_GM_mask_orig = tmp_dir + '/T1_brain_GM_mask_orig.nii.gz'
- T1_brain_WM_mask_orig = tmp_dir + '/T1_brain_WM_mask_orig.nii.gz'
- lmask = tmp_dir + '/lmask.nii.gz'
- rmask = tmp_dir + '/rmask.nii.gz'
- T1_tmp_7 = tmp_dir + '/T1_tmp_7.nii.gz'
+ T1_brain_GM_mask_orig = op.join(tmp_dir, 'T1_brain_GM_mask_orig.nii.gz')
+ T1_brain_WM_mask_orig = op.join(tmp_dir, 'T1_brain_WM_mask_orig.nii.gz')
+ lmask = op.join(tmp_dir, 'lmask.nii.gz')
+ rmask = op.join(tmp_dir, 'rmask.nii.gz')
+ T1_tmp_7 = op.join(tmp_dir, 'T1_tmp_7.nii.gz')
- if not os.path.exists(T1_orig_ud_warp_inv):
+ if not op.exists(T1_orig_ud_warp_inv):
wrappers.invwarp(ref=T1_orig, warp=T1_orig_ud_warp,
out=T1_orig_ud_warp_inv)
diff --git a/bip/pipelines/struct_T1/T1_QC_COG.py b/bip/pipelines/struct_T1/T1_QC_COG.py
index 7236b28349407422b7780455aea77591b9e6a6fe..89d82fe63a2c73718eb84a319421108fdc63eb4d 100755
--- a/bip/pipelines/struct_T1/T1_QC_COG.py
+++ b/bip/pipelines/struct_T1/T1_QC_COG.py
@@ -9,11 +9,12 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os.path as op
import logging
import numpy as np
import nibabel as nib
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
@@ -25,10 +26,10 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- T1_tmp_5 = tmp_dir + '/T1_tmp_5.nii.gz'
- T1_tmp_6 = tmp_dir + '/T1_tmp_6.nii.gz'
+ T1_tmp_5 = op.join(tmp_dir, 'T1_tmp_5.nii.gz')
+ T1_tmp_6 = op.join(tmp_dir, 'T1_tmp_6.nii.gz')
refSubj = ctx.get_data('MNI/MNI152_T1_1mm_BigFoV_facemask.nii.gz')
diff --git a/bip/pipelines/struct_T1/T1_brain_extract.py b/bip/pipelines/struct_T1/T1_brain_extract.py
index c068ef1413328765a0825c2567d30866a6f5703b..f4b1d03329734ecbaaa75bff07f262c9a4481efa 100755
--- a/bip/pipelines/struct_T1/T1_brain_extract.py
+++ b/bip/pipelines/struct_T1/T1_brain_extract.py
@@ -10,11 +10,11 @@
# pylint: disable=W0613
#
-
+import os.path as op
import logging
from shutil import copyfile
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
@@ -40,13 +40,14 @@ def run(ctx,
T1_to_MNI_warp_coef: Out,
T1_to_MNI_warp_jac: Out):
- with redirect_logging(job_name(run), outdir=logs_dir), tempdir(tmp_dir):
+ with redirect_logging(job_name(run), outdir=logs_dir),
+ tempdir(op.join(tmp_dir, job_name(run))):
- T1_tmp_1 = tmp_dir + '/T1_tmp_1.nii.gz'
- T1_tmp_2 = tmp_dir + '/T1_tmp_2.nii.gz'
- T1_tmp_1_brain = tmp_dir + '/T1_tmp_1_brain.nii.gz'
- T1_tmp_orig_ud_to_std_mat = tmp_dir + '/T1_tmp_to_std.mat'
- T1_tmp = tmp_dir + '/T1.nii.gz'
+ T1_tmp_1 = op.join(tmp_dir, 'T1_tmp_1.nii.gz')
+ T1_tmp_2 = op.join(tmp_dir, 'T1_tmp_2.nii.gz')
+ T1_tmp_1_brain = op.join(tmp_dir, 'T1_tmp_1_brain.nii.gz')
+ T1_tmp_orig_ud_to_std_mat = op.join(tmp_dir, 'T1_tmp_to_std.mat')
+ T1_tmp = op.join(tmp_dir, 'T1.nii.gz')
#Calculate where does the brain start in the z dimension and extract the roi
head_top=int(round(float(wrappers.robustfov(T1_orig_ud).stdout[0].split()[7])))
@@ -66,16 +67,16 @@ def run(ctx,
#Generate the actual affine from the orig_ud volume to the cut version
#we haveand combine it to have an affine matrix from orig_ud to MNI
wrappers.flirt(src=T1, ref=T1_orig_ud, omat=T1_to_T1_orig_ud_mat,
- schedule = ctx.FSLDIR + '/etc/flirtsch/xyztrans.sch')
+ schedule = op.join(ctx.FSLDIR, 'etc', 'flirtsch', 'xyztrans.sch')
wrappers.invxfm(inmat=T1_to_T1_orig_ud_mat, omat=T1_orig_ud_to_T1_mat)
- wrappers.concatxfm(atob=T1_to_T1_orig_ud_mat, btoc=T1_orig_ud_to_std_mat,
+ wrappers.concatxfm(atob=T1_to_T1_orig_ud_mat,btoc=T1_orig_ud_to_std_mat,
atoc=T1_to_MNI_linear_mat)
#Non-linear registration to MNI using the previously calculated alignment
wrappers.fnirt(src = T1, ref = ctx.MNI, aff = T1_to_MNI_linear_mat,
config = ctx.get_data('fnirt/bb_fnirt.cnf'),
refmask = ctx.get_data('MNI/MNI152_T1_1mm_brain_mask_dil_GD7.nii.gz'),
- logout = logs_dir + '/bb_T1_to_MNI_fnirt.log',
+ logout = op.join(logs_dir, 'bb_T1_to_MNI_fnirt.log'),
cout = T1_to_MNI_warp_coef, fout = T1_to_MNI_warp,
jout = T1_to_MNI_warp_jac, iout = T1_tmp_2,
interp = 'spline')
diff --git a/bip/pipelines/struct_T1/T1_defacing.py b/bip/pipelines/struct_T1/T1_defacing.py
index 129c20e919f607883ee0515197de5cf47faf87a8..da4ed929f0c7d0f203fd241bb78e6d7e191b5bb3 100755
--- a/bip/pipelines/struct_T1/T1_defacing.py
+++ b/bip/pipelines/struct_T1/T1_defacing.py
@@ -9,10 +9,11 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os.path as op
import logging
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
log = logging.getLogger(__name__)
@@ -29,10 +30,10 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- T1_tmp_4 = tmp_dir + '/T1_tmp_4.nii.gz'
- T1_tmp_mat = tmp_dir + '/T1_tmp.mat'
+ T1_tmp_4 = op.join(tmp_dir, 'T1_tmp_4.nii.gz')
+ T1_tmp_mat = op.join(tmp_dir, 'T1_tmp.mat')
#TODO: Replace this part with proper call to fsl_deface
#Defacing T1_orig
diff --git a/bip/pipelines/struct_T1/T1_fast.py b/bip/pipelines/struct_T1/T1_fast.py
index db37b28f528ba73384cfe7cc304193f5a698f42b..0eb8095fa5a34b7576358f5a3916b78a84b293fb 100755
--- a/bip/pipelines/struct_T1/T1_fast.py
+++ b/bip/pipelines/struct_T1/T1_fast.py
@@ -10,9 +10,10 @@
# pylint: disable=W0613
#
+import os.path as op
import logging
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
@@ -36,7 +37,7 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
#Run fast
- wrappers.fast(T1_brain, out = T1_fast_dir + '/T1_brain', b=True)
+ wrappers.fast(T1_brain, out = op.join(T1_fast_dir, 'T1_brain'), b=True)
#Binarize PVE masks
wrappers.fslmaths(T1_fast_pve_0).thr(0.5).bin().run(T1_fast_CSF_mask)
diff --git a/bip/pipelines/struct_T1/T1_first.py b/bip/pipelines/struct_T1/T1_first.py
index cb39f91e9efabc785e123cdcfefe3714efe3e4f9..193e1073a9f047f4b5bbd0d10232e927f656ded1 100755
--- a/bip/pipelines/struct_T1/T1_first.py
+++ b/bip/pipelines/struct_T1/T1_first.py
@@ -10,12 +10,13 @@
# pylint: disable=W0613
#
-import os
+import os.symlink
+import os.path as op
import glob
import logging
from pipe_tree import In, Out, Ref
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
log = logging.getLogger(__name__)
@@ -30,15 +31,15 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
# Creates a link inside T1_first to T1_unbiased_brain.nii.gz
- if not os.path.exists(T1_first_unbiased_brain):
- os.symlink(src="../T1_unbiased_brain.nii.gz",
- dst=T1_first_unbiased_brain)
+ if not op.exists(T1_first_unbiased_brain):
+ rel_path = op.relpath(T1_unbiased_brain, T1_first_unbiased_brain)
+ os.symlink(src=rel_path, dst=T1_first_unbiased_brain)
wrappers.run_first_all(input=T1_first_unbiased_brain,
output=T1_first_prefix, b=True)
for f in glob.glob(T1_first_prefix + "-*_first*.nii.gz"):
- if os.path.exists(f):
+ if op.exists(f):
os.remove(f)
for f in glob.glob(T1_first_prefix + "-*_corr*.nii.gz"):
- if os.path.exists(f):
+ if op.exists(f):
os.remove(f)
diff --git a/bip/pipelines/struct_T1/T1_sienax.py b/bip/pipelines/struct_T1/T1_sienax.py
index 6d2be868341c150b52c21f877bbbc97bc2fc8397..eb2230206ba718531e0333394228ffa55e612de8 100755
--- a/bip/pipelines/struct_T1/T1_sienax.py
+++ b/bip/pipelines/struct_T1/T1_sienax.py
@@ -10,10 +10,11 @@
#
import os
+import os.path as op
import logging
from fsl import wrappers
from fsl.transform import affine, flirt
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
@@ -40,21 +41,21 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
-
- T1_tmp_mat_1 = tmp_dir + '/tmp_mat_1.mat'
- T1_tmp_mat_2 = tmp_dir + '/tmp_mat_2.mat'
- T1_tmp_mat_3 = tmp_dir + '/tmp_mat_3.mat'
+ tempdir(op.join(tmp_dir, job_name(run))):
+
+ T1_tmp_mat_1 = op.join(tmp_dir, 'tmp_mat_1.mat')
+ T1_tmp_mat_2 = op.join(tmp_dir, 'tmp_mat_2.mat')
+ T1_tmp_mat_3 = op.join(tmp_dir, 'tmp_mat_3.mat')
FSLDIR = ctx.FSLDIR
FSLDATA = FSLDIR + '/data'
FSLMNI = FSLDATA + '/standard'
- MNI = FSLMNI + '/MNI152_T1_1mm.nii.gz'
- MNI_2mm_brain = FSLMNI + '/MNI152_T1_2mm_brain.nii.gz'
- MNI_2mm_skull = FSLMNI + '/MNI152_T1_2mm_skull.nii.gz'
- MNI_2mm_structseg = FSLMNI + '/MNI152_T1_2mm_strucseg.nii.gz'
- MNI_2mm_segperiph = FSLMNI + '/MNI152_T1_2mm_strucseg_periph.nii.gz'
+ MNI = ctx.get_standard('MNI152_T1_1mm.nii.gz')
+ MNI_2mm_brain = ctx.get_standard('MNI152_T1_2mm_brain.nii.gz')
+ MNI_2mm_skull = ctx.get_standard('MNI152_T1_2mm_skull.nii.gz')
+ MNI_2mm_structseg = ctx.get_standard('MNI152_T1_2mm_strucseg.nii.gz')
+ MNI_2mm_segperiph = ctx.get_standard('MNI152_T1_2mm_strucseg_periph.nii.gz')
report = []
@@ -66,17 +67,17 @@ def run(ctx,
# ${FSLDIR}/data/standard/MNI152_T1_2mm_skull T1_brain_skull
# T1_to_MNI_linear.mat
wrappers.flirt(src=T1_brain, ref=MNI_2mm_brain, omat=T1_tmp_mat_1,
- schedule = ctx.FSLDIR + '/etc/flirtsch/pairreg1.sch',
- interp="trilinear")
+ schedule = op.join(ctx.FSLDIR, 'etc', 'flirtsch', 'pairreg1.sch'),
+ interp="trilinear")
wrappers.flirt(src=T1_sienax_brain_skull, ref=MNI_2mm_skull,
- omat=T1_tmp_mat_2, init=T1_tmp_mat_1, interp="trilinear",
- schedule = ctx.FSLDIR + '/etc/flirtsch/pairreg2.sch')
+ omat=T1_tmp_mat_2, init=T1_tmp_mat_1, interp="trilinear",
+ schedule = op.join(ctx.FSLDIR, 'etc', 'flirtsch', 'pairreg2.sch'))
wrappers.fixscaleskew(inmat1=T1_tmp_mat_1, inmat2=T1_tmp_mat_2,
omat=T1_tmp_mat_3)
wrappers.flirt(src=T1_brain, ref=MNI_2mm_brain,
- omat=T1_sienax_to_MNI_linear_mat, init=T1_tmp_mat_3,
- schedule = ctx.FSLDIR + '/etc/flirtsch/pairreg3.sch',
- interp="trilinear")
+ omat=T1_sienax_to_MNI_linear_mat, init=T1_tmp_mat_3,
+ schedule = op.join(ctx.FSLDIR, 'etc', 'flirtsch', 'pairreg3.sch'),
+ interp="trilinear")
matrix = flirt.readFlirt(T1_to_MNI_linear_mat)
scales = affine.decompose(matrix)[0]
@@ -92,15 +93,18 @@ def run(ctx,
wrappers.applywarp(src=MNI_2mm_segperiph, ref=T1,
w=T1_to_MNI_warp_coef_inv, out=T1_sienax_segperiph,
rel=True, interp='trilinear')
- wrappers.fslmaths(T1_sienax_segperiph).thr(0.5).bin().run(T1_sienax_segperiph)
+ wrappers.fslmaths(T1_sienax_segperiph).thr(0.5).bin().\
+ run(T1_sienax_segperiph)
- wrappers.fslmaths(MNI_2mm_structseg).thr(4.5).bin().run(T1_sienax_segvent)
+ wrappers.fslmaths(MNI_2mm_structseg).thr(4.5).bin().\
+ run(T1_sienax_segvent)
wrappers.applywarp(src=T1_sienax_segvent, ref=T1,
w=T1_to_MNI_warp_coef_inv, out=T1_sienax_segvent,
rel=True, interp='nn')
- wrappers.fslmaths(T1_fast_pve_1).mas(T1_sienax_segperiph).run(T1_sienax_pve_1_segperiph)
+ wrappers.fslmaths(T1_fast_pve_1).mas(T1_sienax_segperiph).\
+ run(T1_sienax_pve_1_segperiph)
V = wrappers.fslstats(T1_sienax_pve_1_segperiph).m.v.run()
xa = float(V[0])
xb = float(V[2])
@@ -112,7 +116,8 @@ def run(ctx,
report.append(f'pgrey {xg} {uxg} (peripheral grey)')
- wrappers.fslmaths(T1_fast_pve_0).mas(T1_sienax_segperiph).run(T1_sienax_pve_0_segperiph)
+ wrappers.fslmaths(T1_fast_pve_0).mas(T1_sienax_segperiph).\
+ run(T1_sienax_pve_0_segperiph)
V = wrappers.fslstats(T1_sienax_pve_0_segperiph).m.v.run()
xa = float(V[0])
xb = float(V[2])
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
index a9ba82cccefde53aac5f4dfee04525362e464e54..3ed955aaabb42603b43932ce1ffde386e245fe09 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py
@@ -12,9 +12,10 @@
#
import os
+import os.path as op
import logging
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
@@ -30,7 +31,7 @@ def run(ctx,
with redirect_logging(job_name(run), outdir=logs_dir):
#Apply bias field correction to T2_FLAIR warped
- if os.path.isfile(T1_fast_brain_bias):
+ if op.isfile(T1_fast_brain_bias):
wrappers.fslmaths(T2_FLAIR).div(T1_fast_brain_bias).run(T2_FLAIR_unbiased)
wrappers.fslmaths(T2_FLAIR_brain).div(T1_fast_brain_bias).run(T2_FLAIR_unbiased_brain)
else:
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py
index d85c2745e45bc6a7b8b619bc58e3a80a0fb3e96c..5d02a50aeb5c1f90e5a986e120e37b3e1bde8b4b 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py
@@ -9,11 +9,12 @@
# pylint: disable=W0613,C0301
#
+import os.path as op
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
index 1fba52cd703e7275591c1bcc2cde5461ba46ca71..79034d2e8b87dfaa63d30dcddd6935fc477a3ae3 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py
@@ -9,10 +9,11 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os.path as op
import logging
from shutil import copyfile
from fsl import wrappers
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
@@ -39,10 +40,10 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- T2_FLAIR_tmp_1_mat = tmp_dir + '/T2_FLAIR_tmp_1.mat'
- T2_FLAIR_tmp_2_mat = tmp_dir + '/T2_FLAIR_tmp_2.mat'
+ T2_FLAIR_tmp_1_mat = op.join(tmp_dir, 'T2_FLAIR_tmp_1.mat')
+ T2_FLAIR_tmp_2_mat = op.join(tmp_dir, 'T2_FLAIR_tmp_2.mat')
#Take T2 to T1 and also the brain mask
wrappers.flirt(src=T2_FLAIR_orig_ud, ref=T1_orig_ud,
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py
index d06e5f2aa1b1a8bf19da9ab71cd42f7da7161923..9a9a3cd3094f0164ad42cf32337c36421182baf0 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py
@@ -10,12 +10,12 @@
# pylint: disable=W0613
#
-
+import os.path as op
import logging
from shutil import copyfile
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging, tempdir
+from bip.utils.log_utils import redirect_logging, tempdir, job_name
log = logging.getLogger(__name__)
@@ -32,10 +32,10 @@ def run(ctx,
tmp_dir: Ref):
with redirect_logging(job_name(run), outdir=logs_dir),\
- tempdir(tmp_dir):
+ tempdir(op.join(tmp_dir, job_name(run))):
- T2_FLAIR_tmp_1 = tmp_dir + '/T2_FLAIR_tmp_1nii.gz'
- T2_FLAIR_tmp_3_mat = tmp_dir + '/T2_FLAIR_tmp_3.mat'
+ T2_FLAIR_tmp_1 = op.join(tmp_dir, 'T2_FLAIR_tmp_1nii.gz')
+ T2_FLAIR_tmp_3_mat = op.join(tmp_dir, 'T2_FLAIR_tmp_3.mat')
BigFoV_mask_mat = 'MNI/MNI_to_MNI_BigFoV_facemask.mat'
BigFoV_mask = 'MNI/MNI152_T1_1mm_BigFoV_facemask'
diff --git a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
index 7d1fed84d9a2baf2897a3dc0bc8c4078cb65c8c2..d4d910b173c7bca8efc3fbeefb871ac8e6d16bc8 100755
--- a/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
+++ b/bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py
@@ -13,7 +13,7 @@
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_asl/asl_get_IDPs.py b/bip/pipelines/struct_asl/asl_get_IDPs.py
index 0a1dd4ebc731e6662e51192d5c00f4773a55959d..fff56fe70357f2e28daa8786217842e391e87727 100755
--- a/bip/pipelines/struct_asl/asl_get_IDPs.py
+++ b/bip/pipelines/struct_asl/asl_get_IDPs.py
@@ -10,9 +10,10 @@
# pylint: disable=W0613,R1718
#
+import os.path as op
import logging
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
log = logging.getLogger(__name__)
@@ -34,8 +35,8 @@ def run(ctx,
regions = set([x[0] for x in asl_format])
for region in regions:
- file_name_1 = ASL_region_analysis_dir + "/" + region + ".csv"
- file_name_2 = ASL_region_analysis_dir + "/" + region + ".txt"
+ file_name_1 = op.join(ASL_region_analysis_dir, region + ".csv")
+ file_name_2 = op.join(ASL_region_analysis_dir, region + ".txt")
with open(file_name_1, 'rt', encoding="utf-8") as f:
file_data = f.read()
@@ -54,7 +55,7 @@ def run(ctx,
row = elem[1]
column = elem[2]
- file_name = ASL_region_analysis_dir + "/" + fil + ".txt"
+ file_name = op.join(ASL_region_analysis_dir, fil + ".txt")
with open(file_name, 'rt', encoding="utf-8") as f:
file_data = [x.strip().split(",") for x in f.readlines()]
diff --git a/bip/pipelines/struct_asl/asl_proc.py b/bip/pipelines/struct_asl/asl_proc.py
index 4f785d42d823ca8ab23c44585d33346ee22b280a..9b3fb6ab6e599f6b7370d0ad3191ecb93b9e0c0d 100755
--- a/bip/pipelines/struct_asl/asl_proc.py
+++ b/bip/pipelines/struct_asl/asl_proc.py
@@ -11,13 +11,14 @@
#
import os
+import os.path as op
import glob
import logging
from shutil import copyfile
from fsl import wrappers
from pipe_tree import In, Out, Ref
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
from bip.utils.read_json_field import read_json_field
log = logging.getLogger(__name__)
@@ -64,7 +65,7 @@ def run(ctx,
###############################################
list_PEDs = []
- for fil in glob.glob(ASL_raw_dir + "/*.json"):
+ for fil in glob.glob(op.join(ASL_raw_dir, "*.json")):
list_PEDs.append(read_json_field(fileName=fil,
fieldName="PhaseEncodingDirection"))
@@ -88,8 +89,11 @@ def run(ctx,
wrappers.fslmerge("t", ASL_label, *list_fils_label)
wrappers.fslmerge("t", ASL_DATA_wrongorder, ASL_label, ASL_control)
- os.symlink("../raw/ASL_M0.nii.gz", CALIB)
- os.symlink("../raw/ASL_M0.json", CALIB_json)
+ rel_path = op.relpath(ASL_M0,CALIB)
+ os.symlink(rel_path, CALIB)
+
+ rel_path = op.relpath(ASL_M0_json, CALIB_json)
+ os.symlink(rel_path, CALIB_json)
TE = read_json_field(fileName=CALIB_json, fieldName="EchoTime",
rounding = 3, multFactor=1000)
diff --git a/bip/pipelines/struct_swMRI/swMRI_gdc.py b/bip/pipelines/struct_swMRI/swMRI_gdc.py
index daa322d8a20573152ba90aa387fc07d18c6bfe0a..a0b700090751a2e51d92547155db9bffa5b342bc 100755
--- a/bip/pipelines/struct_swMRI/swMRI_gdc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_gdc.py
@@ -12,7 +12,7 @@
import logging
from shutil import copyfile
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
log = logging.getLogger(__name__)
diff --git a/bip/pipelines/struct_swMRI/swMRI_proc.py b/bip/pipelines/struct_swMRI/swMRI_proc.py
index c75c4728d9ffaaa6a7115fd07240898808ccd71c..08c5b20430d93e8d36665740934d98f40d849719 100755
--- a/bip/pipelines/struct_swMRI/swMRI_proc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_proc.py
@@ -11,11 +11,12 @@
#
import os
+import os.path as op
import logging
from shutil import copyfile
from fsl import wrappers
from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
from bip.pipelines.struct_swMRI.swMRI_proc_fnc import combine_magnitude_coils
from bip.pipelines.struct_swMRI.swMRI_proc_fnc import gen_filtered_phase
from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
@@ -63,13 +64,13 @@ def run(ctx,
complex_phase = True
MAG_TE1 = SWI_MAG_TE1_orig
- if os.path.exists(SWI_MAG_TE2_orig):
+ if op.exists(SWI_MAG_TE2_orig):
MAG_TE2 = SWI_MAG_TE2_orig
else:
MAG_TE2 = ""
if num_coils > 0:
- if os.path.exists(SWI_MAG_TE1_C01):
+ if op.exists(SWI_MAG_TE1_C01):
combine_magnitude_coils(MAG_TE1, MAG_TE2, MAG_TE1_dir,
MAG_TE2_dir, num_coils, SOS_TE1,
SOS_TE2, SOS_ratio, R2star, T2star)
@@ -112,7 +113,7 @@ def run(ctx,
#TODO: Change name of SWI to venogram?
for fil in [R2star, T2star, SOS_TE1, SOS_TE2, SOS_ratio, filtered_phase,
SWI]:
- if os.path.exists(fil):
+ if op.exists(fil):
if ctx.gdc != '':
wrappers.applywarp(src=fil, ref=fil, out=fil, rel=True,
w=SWI_TOTAL_MAG_orig_ud_warp,
diff --git a/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py b/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py
index 17afae1bf3c6ee05f6b7a56026693e88ac9077c8..3e957ee0242072ec2e30641dd535d08d8335f953 100755
--- a/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py
+++ b/bip/pipelines/struct_swMRI/swMRI_proc_fnc.py
@@ -9,6 +9,7 @@
# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
#
+import os.path as op
import glob
import nibabel as nib
from fsl import wrappers
@@ -34,13 +35,13 @@ def combine_magnitude_coils(MAG_TE1, MAG_TE2, MAG_TE1_dir, MAG_TE2_dir,
if not num_coils == 0:
- files_TE1 = glob.glob(MAG_TE1_dir + '/*.nii.gz')
+ files_TE1 = glob.glob(op.join(MAG_TE1_dir, '*.nii.gz'))
wrappers.fslmaths(files_TE1[0]).mul(0).run(SOS_TE1)
for file_TE1 in files_TE1:
wrappers.fslmaths(file_TE1).sqr().add(SOS_TE1).run(SOS_TE1)
wrappers.fslmaths(SOS_TE1).sqrt().run(SOS_TE1)
- files_TE2 = glob.glob(MAG_TE2_dir + '/*.nii.gz')
+ files_TE2 = glob.glob(op.join(MAG_TE2_dir, '*.nii.gz'))
wrappers.fslmaths(files_TE2[0]).mul(0).run(SOS_TE2)
for file_TE2 in files_TE2:
wrappers.fslmaths(file_TE2).sqr().add(SOS_TE2).run(SOS_TE2)
@@ -57,8 +58,8 @@ def combine_magnitude_coils(MAG_TE1, MAG_TE2, MAG_TE1_dir, MAG_TE2_dir,
def gen_filtered_phase(ctx, magImgDir, phaImgDir, magImgFileName, fp_fn,SWI_fn):
- magImgFiles=glob.glob(magImgDir + '/*.nii.gz')
- phaImgFiles=glob.glob(phaImgDir + '/*.nii.gz')
+ magImgFiles=glob.glob(op.join(magImgDir, '*.nii.gz'))
+ phaImgFiles=glob.glob(op.join(phaImgDir, '*.nii.gz'))
magImgFiles.sort()
phaImgFiles.sort()