so the up shot is that after align_epi_anat.py is finished I have to run 3dWarp -deoblique on both func+orig and anat_al+orig to eliminate the obliquity warnings?

With respect to the the timeshifting issue I don't actually have the slice time numbers and getting them is a real PITA.

I presume that 3dTshift -tpattern, will in tha absence of timing info the header will simply assume that the slices are TR/nslices apart. Is that correct?

The patch to align_epi_anat.py is below.

--- align_epi_anat.py.orig 2009-02-20 15:53:44.659133131 +0000
+++ align_epi_anat.py 2009-02-20 16:03:14.301636707 +0000
@@ -212,6 +212,9 @@
(0/mean/median/max/subbrick#)

-tshift : do time shifting of EPI dataset before alignment ([on]/off)
+ -force_ts : Perform timeshifting even if the EPI header indiciates it
+ should not be done. (on/[off])
+ Only use this if you know what you're doing.
-tshift_opts : options to use with 3dTshift
The script will determine if slice timing correction is
necessary unless tshift is set to off.
@@ -337,6 +340,7 @@
self.prep_only = 0 # do preprocessing only
self.odir = os.getcwd()
self.tshift_flag = 1 # do time shifting on EPI
+ self.force_ts_flag = 0 # do time shifting on EPI even if the headers indicate it should not be done
self.volreg_flag = 1 # do volume registration on EPI
self.resample_flag = 1 # do resample
self.deoblique_flag = 1 # deoblique datasets first
@@ -466,6 +470,7 @@

# do time shifting
self.valid_opts.add_opt('-tshift', 1, [], ['on','off'])
+ self.valid_opts.add_opt('-force_ts', 1, [], ['on','off'])
self.valid_opts.add_opt('-tshift_opts', -1, [])

# obliquity options
@@ -713,6 +718,16 @@
self.error_msg("tshift option not on/off")
self.ciao(1)

+ opt = opt_list.find_opt('-force_ts') # do time shifting
+ if opt != None:
+ if(opt.parlist[0]=='on'):
+ self.force_ts_flag = 1
+ elif(opt.parlist[0]=='off'):
+ self.force_ts_flag = 0
+ else:
+ self.error_msg("force_ts option not on/off")
+ self.ciao(1)
+
opt = opt_list.find_opt('-volreg') # do volume registration
if opt != None:
if(opt.parlist[0]=='on'):
@@ -1232,15 +1247,18 @@

# determine if dataset has time shifts in slices
def tshiftable_dset( self, dset=None) :
- com = shell_com( \
- "3dAttribute TAXIS_OFFSETS %s" % dset.input(), ps.oexec,capture=1)
- com.run()
- if ps.dry_run():
- return (1)
- if(len(com.so)): status = 1
- else: status = 0
- return (status)
-
+ if self.force_ts_flag:
+ return 1
+ else:
+ com = shell_com( \
+ "3dAttribute TAXIS_OFFSETS %s" % dset.input(), ps.oexec,capture=1)
+ com.run()
+ if ps.dry_run():
+ return (1)
+ if(len(com.so)): status = 1
+ else: status = 0
+ return (status)
+
# determine if dataset is oblique
def oblique_dset( self, dset=None) :
com = shell_com( \