Thank you for the suggestions, I have tried both:
For 1. It seems to have failed again with the same error, I have placed the stdout below.
For 2. I am able to load the file into Slicer in the sense that it shows up in the Data module. However, as soon as I enable 3D view and try to display the model it crashes. I believe that may have something to do with the graphics capabilities of this workstation, and I am hoping it is not due to data formatting.
Once again, thank you for your time and help!
[rpl6@civmcluster1 large_files_TO_DELETE]$ python2 ~/python_lib/bin/wm_preprocess_all.py -f 10000 -l 10 -j 1 . ./out
Importing whitematteranalysis package.
wm_laterality. Starting white matter laterality computation.
=====input directory======
.
=====output directory=====
./out
==========================
fibers to retain per subject: 10000
minimum length of fibers to retain (in mm): 10
CPUs detected: 16
Using N jobs: 1
==========================
<wm_preprocess.py> Input number of files: 4
('<wm_preprocess.py> ', 1, '/', 4, '**Starting subject:', 'roi_106_tracks')
('<wm_preprocess.py> ', 1, '/', 4, '**Reading input:', 'roi_106_tracks')
('<wm_preprocess.py> ', 1, '/', 4, '**Preprocessing:', 'roi_106_tracks')
Traceback (most recent call last):
File "/home/rpl6/python_lib/bin/wm_preprocess_all.py", line 162, in <module>
for sidx in range(0, len(inputPolyDatas)))
File "/home/rpl6/python_lib/lib/python2.7/site-packages/joblib/parallel.py", line 921, in __call__
if self.dispatch_one_batch(iterator):
File "/home/rpl6/python_lib/lib/python2.7/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch
self._dispatch(tasks)
File "/home/rpl6/python_lib/lib/python2.7/site-packages/joblib/parallel.py", line 716, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/home/rpl6/python_lib/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 182, in apply_async
result = ImmediateResult(func)
File "/home/rpl6/python_lib/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 549, in __init__
self.results = batch()
File "/home/rpl6/python_lib/lib/python2.7/site-packages/joblib/parallel.py", line 225, in __call__
for func, args, kwargs in self.items]
File "/home/rpl6/python_lib/bin/wm_preprocess_all.py", line 120, in pipeline
wm2 = wma.filter.preprocess(wm, args.fiberLength, verbose=False)
File "/home/rpl6/python_lib/lib/python2.7/site-packages/whitematteranalysis/filter.py", line 241, in preprocess
outpd = mask(inpd, fiber_mask, preserve_point_data=preserve_point_data, preserve_cell_data=preserve_cell_data, verbose=verbose)
File "/home/rpl6/python_lib/lib/python2.7/site-packages/whitematteranalysis/filter.py", line 435, in mask
point = inpoints.GetPoint(ptids.GetId(pidx))
ValueError: expects 0 <= id && id < GetNumberOfPoints()