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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

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Nicholas Balderston
June 18, 2018 03:02PM
Hi everyone,

I am having trouble running meica.py with default options. Background... I am running analyses on the NIH biowulf computing cluster, which recently upgraded the OS and some software, which may be part of the problem. I am getting the following error, which seems to occur when trying to run the t2smap.py script. It only happens for one subject/run, but there doesn't seem to be anything special about this subject/run. 

/usr/local/Anaconda/envs/py2.7/lib/python2.7/site-packages/numpy/core/_methods.py:138: RuntimeWarning: invalid value encountered in sqrt
  ret = um.sqrt(ret, out=ret)
/usr/local/apps/afni/current/linux_centos_7_64/meica.libs/t2smap.py:184: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.
  beta,res,rank,sing = np.linalg.lstsq(X,B)
Traceback (most recent call last):
  File "/usr/local/apps/afni/current/linux_centos_7_64/meica.libs/t2smap.py", line 264, in <module>
    s0_maskmin = scoreatpercentile(np.unique(s0),98)/10
  File "/usr/local/apps/afni/current/linux_centos_7_64/meica.libs/t2smap.py", line 35, in scoreatpercentile
    score = values[idx]
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Any help would be greatly appreciated!
thanks,
-nick
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Subject Author Posted

Error in t2smap.py script (meica.py-related)

Nicholas Balderston June 18, 2018 03:02PM

Re: Error in t2smap.py script (meica.py-related)

rick reynolds June 19, 2018 09:45AM