Hi!
I wanna use datagrabber in my Npype workflow but I’m running into som problems. It works fine right now when I’m running:
dg = Node(DataGrabber(infields=['subject_id', 'session_id' ],
outfields=['FLAIR', 'ADC', 't2star']),
name='datagrabber')
# Location of the dataset folder
dg.inputs.base_directory = '/home/brain/Documents/data/iNPH/BIDS/bids_nii/'
# Necessary default parameters
dg.inputs.template = '*'
dg.inputs.sort_filelist = True
dg.inputs.field_template = {'FLAIR': 'sub-%s/ses-1/anat/*FLAIR.nii.gz',
'ADC': 'sub-%s/ses-1/dwi/*adc.nii.gz',
't2star': 'sub-%s/ses-1/func/*T2star.nii.gz'}
dg.inputs.template_args['FLAIR'] = [['subject_id']]
dg.inputs.template_args['ADC'] = [['subject_id']]
dg.inputs.template_args['t2star'] = [['subject_id']]
Worth to mention is that I have the IdentityInterface node which iterate over my subjects.
infosource = Node(IdentityInterface(fields=['subject_id', 'session_id']),
name="infosource")
infosource.iterables = [('subject_id', subject_list),
('session_id', ses_list)]
But as you can see, I’ve set the datagrabber to take data from ses-1 manually in field_template. What I really wanna do is to iterate over my different sessions the same way I iterate over my subjects.
Like: dg.inputs.field_template = {'FLAIR': 'sub-%s/ses-%s/anat/*FLAIR.nii.gz',
Anyone that could help me out?
Sencerely, Jesper