[pymvpa] Group analysis - surface searchlight
Mike E. Klein
michaeleklein at gmail.com
Sat Apr 11 22:53:26 UTC 2015
Hi Nick and PyMVPA group,
I’m trying to run a sample top-level analysis on surface-based searchlight
data using Nick’s afni_surface_alphasim script. I’ve never tried this
before, and am getting a ZeroDivisionError (bottom of output). I tried
re-running the script, leaving out some subjects (in case there is a bad
file/vertex somewhere), but get the same result. Any ideas in how I might
be go about de-bugging this?
Thanks,
Mike
Here is my bash input/output:
*python
/Users/mikeeklein/anaconda/lib/python2.7/site-packages/mvpa2/support/afni/afni_surface_alphasim.py
-d
05/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
06/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
07/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
08/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
09/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
10/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
11/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
12/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
13/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
14/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
15/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
-o groupSurface/ -t 2.3*
** Will execute the following commands:
** - cd "/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface"
** - 3dbucket -overwrite -prefix ./alphasim_buck.niml.dset
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/05/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/06/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/07/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/08/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/09/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/10/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/11/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/12/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/13/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/14/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/15/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset'[0]'
** - 3dTstat -overwrite -prefix ./alphasim_mean.niml.dset
./alphasim_buck.niml.dset
** - echo >
"/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D"
** - 3dcalc -overwrite -prefix ./alphasim_resid_0.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[0]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_0.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_1.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[1]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_1.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_2.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[2]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_2.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_3.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[3]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_3.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_4.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[4]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_4.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_5.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[5]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_5.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_6.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[6]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_6.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_7.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[7]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_7.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_8.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[8]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_8.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_9.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[9]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_9.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
** - 3dcalc -overwrite -prefix ./alphasim_resid_10.niml.dset -a
./alphasim_mean.niml.dset -b ./alphasim_buck.niml.dset'[10]' -expr 'a-b'
** - 3dFWHMx ./alphasim_resid_10.niml.dset | cut -c18- >>
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
**>> Starting now:
++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
** FATAL ERROR: Dataset
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/06/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
differs in size from first one
** Program compile date = May 1 2014
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset has 1 sub-brick ==> -tdiff is turned off
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
++ Output dataset ./alphasim_mean.niml.dset
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././alphasim_resid_0.niml.dset
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 1 is out of range 0..0
** ERROR: bad sub-brick selector [1] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[1]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_1.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 2 is out of range 0..0
** ERROR: bad sub-brick selector [2] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[2]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_2.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 3 is out of range 0..0
** ERROR: bad sub-brick selector [3] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[3]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_3.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 4 is out of range 0..0
** ERROR: bad sub-brick selector [4] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[4]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_4.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 5 is out of range 0..0
** ERROR: bad sub-brick selector [5] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[5]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_5.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 6 is out of range 0..0
** ERROR: bad sub-brick selector [6] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[6]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_6.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 7 is out of range 0..0
** ERROR: bad sub-brick selector [7] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[7]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_7.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 8 is out of range 0..0
** ERROR: bad sub-brick selector [8] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[8]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_8.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 9 is out of range 0..0
** ERROR: bad sub-brick selector [9] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[9]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_9.niml.dset'
** Program compile date = May 1 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: A cast of thousands
** ERROR: selector index 10 is out of range 0..0
** ERROR: bad sub-brick selector [10] => using [0..0]
** FATAL ERROR: can't open dataset ./alphasim_buck.niml.dset[10]
** Program compile date = May 1 2014
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (May 1 2014) [64-bit]
++ Authored by: The Bob
** FATAL ERROR: Can't open dataset './alphasim_resid_10.niml.dset'
** Program compile date = May 1 2014
**<< ... completed execution
[]
/Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/groupSurface/./alphasim_fwhm.1D
Traceback (most recent call last):
File
"/Users/mikeeklein/anaconda/lib/python2.7/site-packages/mvpa2/support/afni/afni_surface_alphasim.py",
line 507, in <module>
run_all(c)
File
"/Users/mikeeklein/anaconda/lib/python2.7/site-packages/mvpa2/support/afni/afni_surface_alphasim.py",
line 382, in run_all
critical_clustersize(config)
File
"/Users/mikeeklein/anaconda/lib/python2.7/site-packages/mvpa2/support/afni/afni_surface_alphasim.py",
line 283, in critical_clustersize
compute_fwhm(config)
File
"/Users/mikeeklein/anaconda/lib/python2.7/site-packages/mvpa2/support/afni/afni_surface_alphasim.py",
line 135, in compute_fwhm
config['fwhm'] = sum(map(float, fwhms)) / len(fwhms) # average FWHM
ZeroDivisionError: integer division or modulo by zero
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