AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
January 12, 2009 05:29PM
I've tried with the newer version and still having problem

[yangming@taipei SN01_S2_RS]$ align_epi_anat.py -anat SN01_S2_EXP_MP_S_oblique+orig -epi SN01_S2_EXP_EP+orig -epi_base 0 -anat_has_skull no -epi_strip None
#++ align_epi_anat version: 1.17
#Script is running:
3dAttribute DELTA /home/yangming/OrientationSel/SN01_S2_RS/SN01_S2_EXP_EP+orig
#++ Spacing for EPI to tlrc alignment is 2.500000 mm
#Script is running (command trimmed):
3dAttribute DELTA SN01_S2_EXP_MP_S_oblique+orig
#++ Spacing for anat to EPI deobliquing is 0.500000 mm
#++ Removing all the temporary files
#Script is running:
rm -f __tt_SN01_S2_EXP_EP*
#Script is running:
rm -f __tt_SN01_S2_EXP_MP_S_oblique*
#Script is running (command trimmed):
3dcopy SN01_S2_EXP_MP_S_oblique+orig __tt_SN01_S2_EXP_MP_S_oblique
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Jan 7 2009) [32-bit]
#Script is running (command trimmed):
3dinfo __tt_SN01_S2_EXP_MP_S_oblique+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/yangming/OrientationSel/SN01_S2_RS/__tt_SN01_S2_EXP_MP_S_oblique+orig is not oblique
#Script is running (command trimmed):
3dinfo SN01_S2_EXP_EP+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/yangming/OrientationSel/SN01_S2_RS/SN01_S2_EXP_EP+orig is ***oblique****
#++ Matching obliquity of anat to epi
#++ Matching obliquity of anat to epi
#Script is running (command trimmed):
3dWarp -verb -card2oblique SN01_S2_EXP_EP+orig -prefix __tt_SN01_S2_EXP_MP_S_oblique_ob -newgrid 0.500000 __tt_SN01_S2_EXP_MP_S_oblique+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > __tt_SN01_S2_EXP_MP_S_oblique_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_2008_07_18_1710 (Jan 7 2009) [32-bit]
++ Authored by: RW Cox
++ Output dataset ./__tt_SN01_S2_EXP_MP_S_oblique_ob+orig.BRIK
#Script is running (command trimmed):
3dAttribute TAXIS_OFFSETS SN01_S2_EXP_EP+orig
#++ Correcting for slice timing
#Script is running (command trimmed):
3dTshift -prefix __tt_SN01_S2_EXP_EP_tsh -cubic SN01_S2_EXP_EP+orig
++ 3dTshift: AFNI version=AFNI_2008_07_18_1710 (Jan 7 2009) [32-bit]
#++ Volume registration for epi data
#Script is running (command trimmed):
3dvolreg -1Dfile __tt_SN01_S2_EXP_EP_tsh_vr_motion.1D -1Dmatrix_save __tt_SN01_S2_EXP_EP_tsh_vr_mat.aff12.1D -prefix __tt_SN01_S2_EXP_EP_tsh_vr -base 0 -cubic__tt_SN01_S2_EXP_EP_tsh+orig
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Jan 7 2009) [32-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 2.73 (mm) at sub-brick 2069
#++ Creating representative epi sub-brick
#Script is running (command trimmed):
3dbucket -prefix __tt_SN01_S2_EXP_EP_tsh_vr_ts __tt_SN01_S2_EXP_EP_tsh_vr+orig'[0]'
++ 3dbucket: AFNI version=AFNI_2008_07_18_1710 (Jan 7 2009) [32-bit]
#++ resampling epi to match anatomical data
#Script is running (command trimmed):
3dresample -master __tt_SN01_S2_EXP_MP_S_oblique_ob+orig -prefix __tt_SN01_S2_EXP_EP_tsh_vr_ts_rs -inset __tt_SN01_S2_EXP_EP_tsh_vr_ts+orig'' -rmode Cu
#++ removing skull or area outside brain
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 __tt_SN01_S2_EXP_EP_tsh_vr_ts_rs+orig
Error: Empty output.
Traceback (most recent call last):
File "/home/yangming/abin/align_epi_anat.py", line 2396, in ?
ps.binmask, ps.perc, -1, suf = "_wt")
File "/home/yangming/abin/align_epi_anat.py", line 1986, in create_weight
th = float(com.val(0,1))
TypeError: float() argument must be a string or a number
Subject Author Posted

align_epi_anat.py problem

Yang-Ming January 12, 2009 10:17AM

Re: align_epi_anat.py problem

Daniel Glen January 12, 2009 10:54AM

Re: align_epi_anat.py problem

Yang-Ming January 12, 2009 03:59PM

Re: align_epi_anat.py problem

Daniel Glen January 12, 2009 04:03PM

Re: align_epi_anat.py problem

Yang-Ming January 12, 2009 04:28PM

Re: align_epi_anat.py problem

Daniel Glen January 12, 2009 04:50PM

Re: align_epi_anat.py problem

Yang-Ming January 12, 2009 05:29PM

Re: align_epi_anat.py problem

Daniel Glen January 13, 2009 10:57AM

Re: align_epi_anat.py problem

Yang-Ming January 13, 2009 11:37AM

Re: align_epi_anat.py problem

Yang-Ming January 13, 2009 11:49AM

Re: align_epi_anat.py problem

Daniel Glen January 13, 2009 12:57PM

Re: align_epi_anat.py problem

Daniel Glen January 14, 2009 04:17PM

Re: align_epi_anat.py problem

Yang-Ming February 04, 2009 10:33AM

Re: align_epi_anat.py problem

Daniel Glen February 04, 2009 12:20PM