def coreg(sbref_image):
#take brain extracted anat as an input, but do not use it
#only to force the pipeline to run brain extraction first
import ants, os, re
#the trick is to get the anat image without the solicit from the pipeline
cwd = os.getcwd()
subj_no = re.findall('\d+',cwd)[-1]
img = '/media/amr/Amr_4TB/NARPS/workingdir_narps_preproc_preproc/preproc/_subject_id_sub-{0}/brain_extraction_anat/highres001_BrainExtractionBrain.nii.gz'.format(subj_no)
fixed = ants.image_read(img)
moving = ants.image_read(sbref_image)
#you have to setup the outprefix, otherwise it will send the output to tmp folder
mytx = ants.registration(fixed=fixed , moving=moving, type_of_transform='Rigid', outprefix = 'sbref_2_anat_sub-{0}'.format(subj_no))
mywarpedimage = ants.apply_transforms(fixed=fixed, moving=moving,
transformlist=mytx['fwdtransforms'])
ants.image_write(image=mywarpedimage, filename='sbref_2_anat_sub-{0}.nii.gz'.format(subj_no))
composite_transform = os.path.abspath('sbref_2_anat_sub-{0}0GenericAffine.mat'.format(subj_no))
warped_image = os.path.abspath('sbref_2_anat_sub-{0}.nii.gz'.format(subj_no))
return composite_transform, warped_image #always you need return
def coreg(bold_image):
#take brain extracted anat as an input, but do not use it
#only to force the pipeline to run brain extraction first
import ants, os, re
import nipype.interfaces.fsl as fsl
#the trick is to get the anat image without the solicit from the pipeline
cwd = os.getcwd()
subj_no = re.findall('\d+',cwd)[-1]
img = '/home/in/aeed/poldrack_gabmling/workingdir_MGT_poldrack_preproc_preproc/preproc/_subject_id_sub-{0}/brain_extraction_anat/sub-{0}_T1w_brain.nii.gz'.format(subj_no)
fixed = ants.image_read(img)
moving = ants.image_read(bold_image)
#you have to setup the outprefix, otherwise it will send the output to tmp folder
mytx = ants.registration(fixed=fixed , moving=moving, type_of_transform='Rigid', outprefix = 'bold_2_anat_sub-{0}'.format(subj_no))
mywarpedimage = ants.apply_transforms(fixed=fixed, moving=moving,
transformlist=mytx['fwdtransforms'])
ants.image_write(image=mywarpedimage, filename='bold_2_anat_sub-{0}.nii.gz'.format(subj_no))
composite_transform = os.path.abspath('bold_2_anat_sub-{0}0GenericAffine.mat'.format(subj_no))
warped_image = os.path.abspath('bold_2_anat_sub-{0}.nii.gz'.format(subj_no))
return composite_transform, warped_image #always you need return
def coreg(bold_image):
# take brain extracted anat as an input, but do not use it
# only to force the pipeline to run brain extraction first
import ants
import os
import re
import nipype.interfaces.fsl as fsl
# the trick is to get the anat image without the solicit from the pipeline
cwd = os.getcwd()
subj_no = re.findall('\d+', cwd)[-1]
img = '/media/amr/Amr_4TB/Work/stimulation/Data_CA3/{0}/Anat_{0}_bet.nii.gz'.format(
subj_no)
fixed = ants.image_read(img)
moving = ants.image_read(bold_image)
# you have to setup the outprefix, otherwise it will send the output to tmp folder
mytx = ants.registration(fixed=fixed,
moving=moving,
type_of_transform='Rigid',
aff_metric='GC',
outprefix='bold_2_anat_sub-{0}'.format(subj_no))
mywarpedimage = ants.apply_transforms(fixed=fixed,
moving=moving,
transformlist=mytx['fwdtransforms'])
ants.image_write(image=mywarpedimage,
filename='bold_2_anat_sub-{0}.nii.gz'.format(subj_no))
# composite_transform = os.path.abspath('bold_2_anat_sub-{0}_0GenericAffine.mat'.format(subj_no))
# warped_image = os.path.abspath('bold_2_anat_sub-{0}.nii.gz'.format(subj_no))
composite_transform = 'bold_2_anat_sub-{0}_0GenericAffine.mat'.format(
subj_no)
warped_image = 'bold_2_anat_sub-{0}.nii.gz'.format(subj_no)
return composite_transform, warped_image # always you need return