Reply To: Problem with smoothing

Forums Forums Surface and Volume Registration (SVReg) Problem with smoothing Reply To: Problem with smoothing

#894
leonidastra86
Participant

Perfect! So far so good. I smoothed both hemispheres and wanted to start the analysis. My demographics file is ready, however I cannot install BSS. I already installed R and R Studio but as soon as I type pip install bss I receive the following problem:

Leonidass-Air:~ leonidastra86$ pip install bss
Collecting bss
Using cached bss-0.9.4-py2.py3-none-any.whl
Collecting matplotlib>=1.5.3 (from bss)
Downloading matplotlib-2.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.2MB)
100% |████████████████████████████████| 13.2MB 89kB/s
Collecting numpy>=1.11 (from bss)
Using cached numpy-1.13.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting statsmodels>=0.6.1 (from bss)
Using cached statsmodels-0.8.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting patsy>=0.4 (from bss)
Using cached patsy-0.4.1-py2.py3-none-any.whl
Collecting scipy>=0.18 (from bss)
Using cached scipy-0.19.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting nibabel>=2.1 (from bss)
Using cached nibabel-2.1.0.zip
Collecting pandas>=0.19 (from bss)
Using cached pandas-0.20.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.5.3->bss)
Requirement already satisfied: pytz in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.5.3->bss)
Collecting backports.functools-lru-cache (from matplotlib>=1.5.3->bss)
Downloading backports.functools_lru_cache-1.4-py2.py3-none-any.whl
Collecting six>=1.10 (from matplotlib>=1.5.3->bss)
Using cached six-1.11.0-py2.py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib>=1.5.3->bss)
Using cached cycler-0.10.0-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib>=1.5.3->bss)
Using cached subprocess32-3.2.7.tar.gz
Collecting python-dateutil>=2.0 (from matplotlib>=1.5.3->bss)
Downloading python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)
100% |████████████████████████████████| 194kB 2.0MB/s
Installing collected packages: numpy, backports.functools-lru-cache, six, cycler, subprocess32, python-dateutil, matplotlib, scipy, patsy, pandas, statsmodels, nibabel, bss
Found existing installation: numpy 1.8.0rc1
DEPRECATION: Uninstalling a distutils installed project (numpy) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
Uninstalling numpy-1.8.0rc1:
Exception:
Traceback (most recent call last):
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/basecommand.py”, line 215, in main
status = self.run(options, args)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/commands/install.py”, line 342, in run
prefix=options.prefix_path,
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_set.py”, line 778, in install
requirement.uninstall(auto_confirm=True)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py”, line 754, in uninstall
paths_to_remove.remove(auto_confirm)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_uninstall.py”, line 115, in remove
renames(path, new_path)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/utils/__init__.py”, line 267, in renames
shutil.move(old, new)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py”, line 302, in move
copy2(src, real_dst)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py”, line 131, in copy2
copystat(src, dst)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py”, line 103, in copystat
os.chflags(dst, st.st_flags)
OSError: [Errno 1] Operation not permitted: ‘/var/folders/13/mblgc8t52kx3g229dsds97r00000gn/T/pip-szRNjk-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info’

As far as I understand it will be installed and afterwards deinstalled. Why?

And one more question, in the USC2015_Brainsuite Workshop there is one more smoothed file in every patient folder, the ABCS.svreg.inv.map.jacdet.smooth2.0mm.nii.gz.

Should I smooth it too? Is it important for the analysis?

Thank you sooo much for your help.