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Nicholas Balderston
October 28, 2015 11:16AM
Hey everyone,

I am starting a new multi echo study on 3TB at NIH. I am trying to get the meica.py script to run (on biowulf2), but am encountering some errors with the tedana.py script. Any ideas?

Here's the command I am using: 
meica.py \
-e 18.4,39.5,60.6 \
-b 10s \
--OVERWRITE \
--daw=-1 \
-d 002.pre_rest_axial_epi.echo_001_dataset+orig,002.pre_rest_axial_epi.echo_001_dataset+orig,002.pre_rest_axial_epi.echo_001_dataset+orig

Here's the output:
Quote
tedana.py
/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py:233: RuntimeWarning: divide by zero encountered in divide
t2s = 1/beta[1,:].transpose()
/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py:36: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
#import ipdb
/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py:104: RuntimeWarning: divide by zero encountered in divide
stdout.write(" + Writing file: %s ...." % name)
/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py:108: RuntimeWarning: invalid value encountered in divide
thishead = head.copy()
/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py:121: RuntimeWarning: invalid value encountered in greater
"""
/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py:400: RuntimeWarning: invalid value encountered in less
kappas_lim = kappas[andb([kappas<fmid,kappas>fmin])==2]
/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py:400: RuntimeWarning: invalid value encountered in greater
kappas_lim = kappas[andb([kappas<fmid,kappas>fmin])==2]
Traceback (most recent call last):
File "/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py", line 603, in <module>
nc,dd = tedpca(options.ste)
File "/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py", line 402, in tedpca
kappa_thr = kappas_lim[getelbow(kappas_lim)]
File "/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py", line 311, in getelbow
p = coords - np.tile(np.reshape(coords[:,0],(2,1)),(1,nc))
IndexError: index 0 is out of bounds for axis 1 with size 0

thanks!
-nick

P.S. Side note... is there a suggested method for analyzing multiple runs? Separate? Concatonated?
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Subject Author Posted

meica.py/tedana.py

Nicholas Balderston October 28, 2015 11:16AM

Re: meica.py/tedana.py

Nicholas Balderston October 28, 2015 11:39AM

Re: meica.py/tedana.py

djangraw October 28, 2015 12:05PM