def recon_all(self,
fs_subject,
prefix='prefix',
args='RECON-ALL ARGS GO HERE!',
helptext='#The helptext was not filled in',
hold_jid=[]):
'''
Generic Freesurfer recon-all command. Will create and submit script to SGE qmon
|fs_subject - FS_Subject object we want to work on
|prefix - text to prepend to script file so we know what operation was carried out
|args - arguments to the recon-all command
|helptext - Descriptive text to put at top of script file
|hold_jid - list of jobids
returns jobid of submitted job as string
'''
#set up template objects
reconalltemplate = os.path.join(self.qsubTemplatesDir, 'reconall.sh')
qsub = Qsub(templatepath=reconalltemplate,
scriptdir=os.path.join(self.path, 'runs_freesurfer'),
qsubpath='qsub',
command_args=['mem_free=3.5G', 'h_vmem=3.5G'])
#set up substitution dictionary
subs_dict = self.__buildDict__(fs_subject=fs_subject,
prefix=prefix,
args=args,
helptext=helptext)
#submit and return jobid
return qsub.submit(subs_dict,
submitted_dir=fs_subject.submitted_dir,
done_dir=fs_subject.done_dir,
hold_jid=hold_jid)
def FS_to_Native_warp(Target,
Movable_Image,
Output,
hold_jid=[],
prefix='FS_to_Native_warp',
fsl_path='/usr/local/aleksey/fsl',
ants_path='/usr/local/aleksey/ANTS/bin'):
visit = Target.visit
prefix = Movable_Image.series + '_FS_to_Native_warp'
qsub = Qsub(templatepath=os.path.join(template_folder,
'FS_to_Native_warp.sh'),
scriptdir=os.path.join(visit.path, 'Qsub'),
qsubpath='qsub',
command_args=['mem_free=2G', 'h_vmem=2G'])
dict = {
'filename':
prefix + '_' + visit.visid + '_' + visit.subject.subid + '.sh',
'subid': visit.subject.subid,
'visid': visit.visid,
'fs_folder': os.path.join(visit.path, Movable_Image.folder),
'Target': Target.path,
'Movable_Image': Movable_Image.path,
'Output': Output.path,
'FSL_PATH': fsl_path,
'ANTS_PATH': ants_path,
}
return qsub.submit(dict, hold_jid=hold_jid) #return jobid as str
