Thanks for sharing that. A couple initial notes:
- It looks like the relevant programs exist there (missing R programs won't affect the
@SUMA_Make_Spec_FS issues).
- That is a pretty old version of AFNI, over three years old now---I'm not sure that updating will fix the current issue, but there will be newer functionality including more supplementary datasets and QC images created automatically.
- Also, having Python's matplotlib module (ver>=2.2.3) would be useful for other areas of AFNI procressing, particular with afni_proc.py's QC HTML.
From the bottom of the system check in the "Please Fix" section, these are a few things you can do, also, which likely won't affect what is happening here, but which will make using AFNI a bit simpler on your system (e.g., being able to autocomplete AFNI program option flags as you type):
* please run: cp /appl/afni_openmp-20.1/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
It's a little odd that afni is owned by root. I also have not seen this before:
ERROR:root:code for hash md5 was not found.
Traceback (most recent call last):
File "/appl/python-2.7.14/lib/python2.7/hashlib.py", line 147, in <module>
globals()[__func_name] = __get_hash(__func_name)
File "/appl/python-2.7.14/lib/python2.7/hashlib.py", line 109, in __get_openssl_constructor
return __get_builtin_constructor(name)
File "/appl/python-2.7.14/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type md5
... I haven't seen that before and I am not sure if it is related here, but that is possible.
It would probably be most helpful to see all the output of @SUMA_Make_Spec_FS, to see where the error first occurred in its processing. Also, as noted here:
Notes on using FreeSurfer with AFNI
... it might be helpful to add one option -fspath .., like here:
@SUMA_Make_Spec_FS \
-fs_setup \
-NIFTI \
-sid SUBJ \
-fspath ./SUBJ
(and using -fs_setup might not matter on your OS, but can be useful on other ones, so I generally leave it in).
Would you be able to re-run @SUMA_Make_Spec_FS with that -fspath .. option, and save all the terminal output to a text file, so we could see the full history? In different types of shells this would be done like:
# if using bash:
@SUMA_Make_Spec_FS ... \
2>&1 | tee output_fs.txt
# if using tcsh/csh:
@SUMA_Make_Spec_FS ... \
|& tee output_fs.txt
... and you can check your local shell by running echo $0.
thanks,
pt
