[zafarneyaz]

zafar@zafar-Lenovo-ideapad-300-15ISK:~/Desktop$ sudo bash install.sh /usr/share/bss
This will install the BrainSuite Statistics toolbox.
This will also install a mini version of anaconda python, R, rpy2, and statsmodels.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 26.5M 100 26.5M 0 0 20679 0 0:22:23 0:22:23 –:–:– 20071
PREFIX=/usr/share/bss
installing: python-2.7.12-1 …
installing: conda-env-2.6.0-0 …
installing: enum34-1.1.6-py27_0 …
installing: openssl-1.0.2j-0 …
installing: pycosat-0.6.1-py27_1 …
installing: readline-6.2-2 …
installing: requests-2.11.1-py27_0 …
installing: ruamel_yaml-0.11.14-py27_0 …
installing: sqlite-3.13.0-0 …
installing: tk-8.5.18-0 …
installing: yaml-0.1.6-0 …
installing: zlib-1.2.8-3 …
installing: conda-4.2.11-py27_0 …
installing: pycrypto-2.6.1-py27_4 …
installing: pip-8.1.2-py27_0 …
installing: wheel-0.29.0-py27_0 …
installing: setuptools-27.2.0-py27_0 …
Python 2.7.12 :: Continuum Analytics, Inc.
creating default environment…
using -f (force) option
installation finished.
Installing BrainSuite statistical toolbox…This may take a few minutes…Fetching package metadata ………….
Solving package specifications: ……….

Package plan for installation in environment /usr/share/bss:

The following packages will be downloaded:

package | build
—————————|—————–
gettext-0.19.7 | 1 5.6 MB conda-forge
gmp-6.1.1 | 0 727 KB conda-forge
icu-56.1 | 4 21.9 MB conda-forge
jpeg-9b | 0 918 KB conda-forge
libffi-3.2.1 | 2 47 KB conda-forge
libgcc-4.8.5 | 1 922 KB r
libgfortran-3.0.0 | 1 281 KB
libiconv-1.14 | 3 2.0 MB conda-forge
libpng-1.6.17 | 0 214 KB
libsodium-1.0.10 | 0 1.5 MB conda-forge
mkl-11.3.3 | 0 122.1 MB
ncurses-5.9 | 9 954 KB conda-forge
pcre-8.38 | 1 631 KB conda-forge
pixman-0.32.6 | 0 3.7 MB conda-forge
xz-5.2.2 | 0 853 KB conda-forge
freetype-2.5.5 | 1 2.5 MB
glib-2.48.0 | 4 4.7 MB conda-forge
hdf5-1.8.15.1 | 3 1.9 MB
libtiff-4.0.6 | 6 507 KB conda-forge
libxml2-2.9.4 | 2 4.9 MB conda-forge
pandoc-1.17.2 | 0 17.3 MB conda-forge
zeromq-4.1.5 | 0 5.0 MB conda-forge
backports.shutil_get_terminal_size-1.0.0| py27_0 5 KB conda-forge
backports_abc-0.4 | py27_0 5 KB conda-forge
certifi-2016.8.31 | py27_0 219 KB conda-forge
conda-env-2.5.2 | py27_0 26 KB conda-forge
configparser-3.5.0 | py27_0 31 KB conda-forge
decorator-4.0.10 | py27_0 12 KB conda-forge
fontconfig-2.11.1 | 6 405 KB
functools32-3.2.3.2 | py27_1 16 KB conda-forge
ipython_genutils-0.1.0 | py27_0 33 KB conda-forge
markupsafe-0.23 | py27_0 31 KB conda-forge
mistune-0.7.3 | py27_0 22 KB conda-forge
numpy-1.9.3 | py27_3 5.7 MB
ptyprocess-0.5.1 | py27_0 19 KB conda-forge
pyparsing-2.0.3 | py27_0 63 KB
pytz-2016.7 | py27_0 161 KB conda-forge
pyyaml-3.11 | py27_0 339 KB conda-forge
pyzmq-16.0.0 | py27_0 806 KB conda-forge
simplegeneric-0.8.1 | py27_0 6 KB conda-forge
sip-4.18 | py27_0 263 KB conda-forge
six-1.10.0 | py27_1 18 KB conda-forge
ssl_match_hostname-3.5.0.1 | py27_0 6 KB conda-forge
traits-4.4.0 | py27_0 421 KB
vtk-5.10.1 | py27_1 92.2 MB
wcwidth-0.1.7 | py27_0 22 KB conda-forge
cairo-1.12.18 | 6 594 KB
conda-4.1.12 | py27_0 200 KB conda-forge
configobj-5.0.6 | py27_0 50 KB
entrypoints-0.2.2 | py27_0 6 KB conda-forge
h5py-2.5.0 | np19py27_3 2.3 MB
jinja2-2.8 | py27_1 282 KB conda-forge
jsonschema-2.5.1 | py27_0 70 KB conda-forge
pathlib2-2.1.0 | py27_0 26 KB conda-forge
pexpect-4.2.1 | py27_0 65 KB conda-forge
pydicom-0.9.9 | py27_0 598 KB conda-forge
pyface-4.4.0 | py27_0 694 KB
pygments-2.1.3 | py27_1 1.2 MB conda-forge
python-dateutil-2.5.3 | py27_0 236 KB conda-forge
scipy-0.17.1 | np19py27_1 30.0 MB
singledispatch-3.4.0.3 | py27_0 12 KB conda-forge
traitlets-4.3.1 | py27_0 121 KB conda-forge
harfbuzz-0.9.35 | 6 1.1 MB r
jupyter_core-4.2.0 | py27_0 56 KB conda-forge
nibabel-2.1.0 | py27_0 2.6 MB conda-forge
pandas-0.17.1 | np19py27_0 12.2 MB
patsy-0.4.1 | py27_0 291 KB conda-forge
pickleshare-0.7.3 | py27_0 8 KB conda-forge
prompt_toolkit-1.0.8 | py27_0 311 KB conda-forge
py2cairo-1.10.0 | py27_2 36 KB
tornado-4.4.2 | py27_0 569 KB conda-forge
traitsui-4.4.0 | py27_0 837 KB
apptools-4.2.1 | py27_0 282 KB
ipython-5.1.0 | py27_1 980 KB conda-forge
jupyter_client-4.4.0 | py27_0 101 KB conda-forge
nbformat-4.1.0 | py27_0 120 KB conda-forge
pango-1.36.8 | 3 796 KB r
statsmodels-0.6.1 | np19py27_0 5.0 MB
terminado-0.6 | py27_0 18 KB conda-forge
envisage-4.4.0 | py27_1 267 KB
ipykernel-4.5.0 | py27_0 128 KB conda-forge
nbconvert-4.2.0 | py27_0 310 KB conda-forge
qt-4.8.7 | 4 32.7 MB
r-base-3.2.2 | 0 20.6 MB r
jupyter_console-5.0.0 | py27_0 28 KB conda-forge
notebook-4.2.3 | py27_0 5.4 MB conda-forge
pyqt-4.11.4 | py27_1 3.5 MB conda-forge
matplotlib-1.4.3 | np19py27_2 44.5 MB
mayavi-4.4.0 | np19py27_0 10.3 MB
qtconsole-4.2.1 | py27_0 132 KB conda-forge
widgetsnbextension-1.2.6 | py27_3 1.1 MB conda-forge
ipywidgets-5.2.2 | py27_2 61 KB conda-forge
jupyter-1.0.0 | py27_3 3 KB
r-3.2.2 | 0 2 KB r
r-bitops-1.0_6 | r3.2.2_1a 22 KB r
r-boot-1.3_17 | r3.2.2_0a 575 KB r
r-chron-2.3_47 | r3.2.2_0a 98 KB r
r-cluster-2.0.3 | r3.2.2_0a 466 KB r
r-codetools-0.2_14 | r3.2.2_0a 45 KB r
r-digest-0.6.8 | r3.2.2_2a 93 KB r
r-foreign-0.8_66 | r3.2.2_0a 220 KB r
r-formatr-1.2.1 | r3.2.2_0a 45 KB r
r-highr-0.5.1 | r3.2.2_0a 30 KB r
r-kernsmooth-2.23_15 | r3.2.2_0a 83 KB r
r-lattice-0.20_33 | r3.2.2_0a 697 KB r
r-magrittr-1.5 | r3.2.2_1a 154 KB r
r-mass-7.3_45 | r3.2.2_0a 1.0 MB r
r-mime-0.4 | r3.2.2_0a 26 KB r
r-nnet-7.3_11 | r3.2.2_0a 99 KB r
r-rpart-4.1_10 | r3.2.2_0a 861 KB r
r-spatial-7.3_11 | r3.2.2_0a 122 KB r
r-stringi-1.0_1 | r3.2.2_0a 10.7 MB r
r-survival-2.38_3 | r3.2.2_0a 4.4 MB r
r-yaml-2.1.13 | r3.2.2_1a 80 KB r
rpy2-2.7.0 | py27r3.2.2_0 357 KB r
r-catools-1.17.1 | r3.2.2_2a 157 KB r
r-class-7.3_14 | r3.2.2_0a 81 KB r
r-data.table-1.9.6 | r3.2.2_0a 1.5 MB r
r-htmltools-0.2.6 | r3.2.2_2a 83 KB r
r-markdown-0.7.7 | r3.2.2_1a 104 KB r
r-matrix-1.2_2 | r3.2.2_0a 3.1 MB r
r-nlme-3.1_122 | r3.2.2_0a 2.0 MB r
r-stringr-1.0.0 | r3.2.2_0a 78 KB r
r-evaluate-0.8 | r3.2.2_0a 39 KB r
r-mgcv-1.8_9 | r3.2.2_0a 1.8 MB r
r-knitr-1.11 | r3.2.2_0a 550 KB r
r-recommended-3.2.2 | r3.2.2_0 707 B r
r-rmarkdown-0.8.1 | r3.2.2_0a 1.1 MB r
bss-v2016f.4 | r3.2.2_0 96 KB bss
————————————————————
Total: 511.1 MB

The following NEW packages will be INSTALLED:

apptools: 4.2.1-py27_0
backports.shutil_get_terminal_size: 1.0.0-py27_0 conda-forge
backports_abc: 0.4-py27_0 conda-forge
bss: v2016f.4-r3.2.2_0 bss
cairo: 1.12.18-6
certifi: 2016.8.31-py27_0 conda-forge
configobj: 5.0.6-py27_0
configparser: 3.5.0-py27_0 conda-forge
decorator: 4.0.10-py27_0 conda-forge
entrypoints: 0.2.2-py27_0 conda-forge
envisage: 4.4.0-py27_1
fontconfig: 2.11.1-6
freetype: 2.5.5-1
functools32: 3.2.3.2-py27_1 conda-forge
gettext: 0.19.7-1 conda-forge
glib: 2.48.0-4 conda-forge
gmp: 6.1.1-0 conda-forge
h5py: 2.5.0-np19py27_3
harfbuzz: 0.9.35-6 r
hdf5: 1.8.15.1-3
icu: 56.1-4 conda-forge
ipykernel: 4.5.0-py27_0 conda-forge
ipython: 5.1.0-py27_1 conda-forge
ipython_genutils: 0.1.0-py27_0 conda-forge
ipywidgets: 5.2.2-py27_2 conda-forge
jinja2: 2.8-py27_1 conda-forge
jpeg: 9b-0 conda-forge
jsonschema: 2.5.1-py27_0 conda-forge
jupyter: 1.0.0-py27_3
jupyter_client: 4.4.0-py27_0 conda-forge
jupyter_console: 5.0.0-py27_0 conda-forge
jupyter_core: 4.2.0-py27_0 conda-forge
libffi: 3.2.1-2 conda-forge
libgcc: 4.8.5-1 r
libgfortran: 3.0.0-1
libiconv: 1.14-3 conda-forge
libpng: 1.6.17-0
libsodium: 1.0.10-0 conda-forge
libtiff: 4.0.6-6 conda-forge
libxml2: 2.9.4-2 conda-forge
markupsafe: 0.23-py27_0 conda-forge
matplotlib: 1.4.3-np19py27_2
mayavi: 4.4.0-np19py27_0
mistune: 0.7.3-py27_0 conda-forge
mkl: 11.3.3-0
nbconvert: 4.2.0-py27_0 conda-forge
nbformat: 4.1.0-py27_0 conda-forge
ncurses: 5.9-9 conda-forge
nibabel: 2.1.0-py27_0 conda-forge
notebook: 4.2.3-py27_0 conda-forge
numpy: 1.9.3-py27_3
pandas: 0.17.1-np19py27_0
pandoc: 1.17.2-0 conda-forge
pango: 1.36.8-3 r
pathlib2: 2.1.0-py27_0 conda-forge
patsy: 0.4.1-py27_0 conda-forge
pcre: 8.38-1 conda-forge
pexpect: 4.2.1-py27_0 conda-forge
pickleshare: 0.7.3-py27_0 conda-forge
pixman: 0.32.6-0 conda-forge
prompt_toolkit: 1.0.8-py27_0 conda-forge
ptyprocess: 0.5.1-py27_0 conda-forge
py2cairo: 1.10.0-py27_2
pydicom: 0.9.9-py27_0 conda-forge
pyface: 4.4.0-py27_0
pygments: 2.1.3-py27_1 conda-forge
pyparsing: 2.0.3-py27_0
pyqt: 4.11.4-py27_1 conda-forge
python-dateutil: 2.5.3-py27_0 conda-forge
pytz: 2016.7-py27_0 conda-forge
pyyaml: 3.11-py27_0 conda-forge
pyzmq: 16.0.0-py27_0 conda-forge
qt: 4.8.7-4
qtconsole: 4.2.1-py27_0 conda-forge
r: 3.2.2-0 r
r-base: 3.2.2-0 r
r-bitops: 1.0_6-r3.2.2_1a r
r-boot: 1.3_17-r3.2.2_0a r
r-catools: 1.17.1-r3.2.2_2a r
r-chron: 2.3_47-r3.2.2_0a r
r-class: 7.3_14-r3.2.2_0a r
r-cluster: 2.0.3-r3.2.2_0a r
r-codetools: 0.2_14-r3.2.2_0a r
r-data.table: 1.9.6-r3.2.2_0a r
r-digest: 0.6.8-r3.2.2_2a r
r-evaluate: 0.8-r3.2.2_0a r
r-foreign: 0.8_66-r3.2.2_0a r
r-formatr: 1.2.1-r3.2.2_0a r
r-highr: 0.5.1-r3.2.2_0a r
r-htmltools: 0.2.6-r3.2.2_2a r
r-kernsmooth: 2.23_15-r3.2.2_0a r
r-knitr: 1.11-r3.2.2_0a r
r-lattice: 0.20_33-r3.2.2_0a r
r-magrittr: 1.5-r3.2.2_1a r
r-markdown: 0.7.7-r3.2.2_1a r
r-mass: 7.3_45-r3.2.2_0a r
r-matrix: 1.2_2-r3.2.2_0a r
r-mgcv: 1.8_9-r3.2.2_0a r
r-mime: 0.4-r3.2.2_0a r
r-nlme: 3.1_122-r3.2.2_0a r
r-nnet: 7.3_11-r3.2.2_0a r
r-recommended: 3.2.2-r3.2.2_0 r
r-rmarkdown: 0.8.1-r3.2.2_0a r
r-rpart: 4.1_10-r3.2.2_0a r
r-spatial: 7.3_11-r3.2.2_0a r
r-stringi: 1.0_1-r3.2.2_0a r
r-stringr: 1.0.0-r3.2.2_0a r
r-survival: 2.38_3-r3.2.2_0a r
r-yaml: 2.1.13-r3.2.2_1a r
rpy2: 2.7.0-py27r3.2.2_0 r
scipy: 0.17.1-np19py27_1
simplegeneric: 0.8.1-py27_0 conda-forge
singledispatch: 3.4.0.3-py27_0 conda-forge
sip: 4.18-py27_0 conda-forge
six: 1.10.0-py27_1 conda-forge
ssl_match_hostname: 3.5.0.1-py27_0 conda-forge
statsmodels: 0.6.1-np19py27_0
terminado: 0.6-py27_0 conda-forge
tornado: 4.4.2-py27_0 conda-forge
traitlets: 4.3.1-py27_0 conda-forge
traits: 4.4.0-py27_0
traitsui: 4.4.0-py27_0
vtk: 5.10.1-py27_1
wcwidth: 0.1.7-py27_0 conda-forge
widgetsnbextension: 1.2.6-py27_3 conda-forge
xz: 5.2.2-0 conda-forge
zeromq: 4.1.5-0 conda-forge

The following packages will be SUPERCEDED by a higher-priority channel:

conda: 4.2.11-py27_0 –> 4.1.12-py27_0 conda-forge
conda-env: 2.6.0-0 –> 2.5.2-py27_0 conda-forge

Fetching packages …
gettext-0.19.7 100% |###############################| Time: 0:05:38 17.42 kB/s
gmp-6.1.1-0.ta 100% |###############################| Time: 0:00:49 15.13 kB/s
icu-56.1-4.tar 100% |###############################| Time: 0:23:19 16.41 kB/s
jpeg-9b-0.tar. 100% |###############################| Time: 0:01:05 14.35 kB/s
libffi-3.2.1-2 100% |###############################| Time: 0:00:01 29.80 kB/s
libgcc-4.8.5-1 100% |###############################| Time: 0:00:59 15.74 kB/s
libgfortran-3. 100% |###############################| Time: 0:00:13 20.99 kB/s
libiconv-1.14- 34% |########## | Time: 0:00:49 14.59 kAn unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:

https://github.com/conda/conda/issues

Current conda install:

platform : linux-64
conda version : 4.2.11
conda is private : False
conda-env version : 4.2.11
conda-build version : not installed
python version : 2.7.12.final.0
requests version : 2.11.1
root environment : /usr/share/bss (writable)
default environment : /usr/share/bss
envs directories : /usr/share/bss/envs
package cache : /usr/share/bss/pkgs
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bss/linux-64
https://conda.anaconda.org/bss/noarch
https://conda.anaconda.org/r/linux-64
https://conda.anaconda.org/r/noarch
https://repo.continuum.io/pkgs/free/linux-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/pro/linux-64
https://repo.continuum.io/pkgs/pro/noarch
config file : /home/zafar/.condarc
offline mode : False

$ /usr/share/bss/bin/conda install bss -y

Traceback (most recent call last):
File “/usr/share/bss/lib/python2.7/site-packages/conda/exceptions.py”, line 479, in conda_exception_handler
return_value = func(*args, **kwargs)
File “/usr/share/bss/lib/python2.7/site-packages/conda/cli/main.py”, line 145, in _main
exit_code = args.func(args, p)
File “/usr/share/bss/lib/python2.7/site-packages/conda/cli/main_install.py”, line 80, in execute
install(args, parser, ‘install’)
File “/usr/share/bss/lib/python2.7/site-packages/conda/cli/install.py”, line 420, in install
raise CondaRuntimeError(‘RuntimeError: %s’ % e)
CondaRuntimeError: Runtime error: RuntimeError: Runtime error: Could not open u’/usr/share/bss/pkgs/libiconv-1.14-3.tar.bz2.part’ for writing (HTTPSConnectionPool(host=’binstar-cio-packages-prod.s3.amazonaws.com’, port=443): Read timed out.).

install.sh: line 67: /usr/share/bss/bin/R: No such file or directory 16.29 kB/s
export PATH=/usr/share/bss/bin/:${PATH}
BrainSuite statistical toolbox was installed successfully.
Cleaning up temporary files…rm: cannot remove ‘/usr/share/bss/tmp/Miniconda2—x86_64.sh’: No such file or directory
Done.

Try running
/usr/share/bss/bin/bss_run.py -h
It should display help and then exit.

zafar@zafar-Lenovo-ideapad-300-15ISK:~/Desktop$

there is no file bss_run.py -h in bin

[zafarneyaz]

thank you very much

[zafarneyaz]

I tried with the new installation file, but the following message came.

An unexpected error has occurred, please consider sending the
following traceback to the conda GitHub issue tracker at:

https://github.com/conda/conda/issues

Include the output of the command ‘conda info’ in your report.

[zafarneyaz]

Please provide a single line command for installation of all components of bss for windows 7 /10, so that less experienced uses may install it

[zafarneyaz]

Hi,
There is no folder named as “directory or “bin” in the scripts folder. However, there is a file in scripts folder named “bss_run.py”. When I try to run the command “python bss_run.py –h” from this folder, the following message comes.

C:\Users>cd C:\Program Files\Miniconda\Scripts
C:\Program Files\Miniconda\Scripts> python bss_run.py -h
Error: DLL load failed: The specified module could not be found.
Something happened during imports.
Perhaps R is not installed properly or R_HOME is not setto the correct version
Please send the whole message to the developers.
C:\Program Files\Miniconda\Scripts>

I have already posted the warning messages during the installation process.
1. Setting R Environment to c:\Program Files\R\R-3.2.2\bin\x64\
WARNING: The data being saved is truncated to 1024 characters.
2. Error in read.dcf(file.path(pkgname, “DESCRIPTION”), c(“Package”, “Type”)) :
cannot open the connection

I am a radiologist and less familiar with computer commands.

Dr. Zafar Neyaz
Associate Professor
Dept. of Radiodiagnosis
SGPGIMS, Lucknow , U.P. – India

[zafarneyaz]

I also have similiar problem… Kindly elaborate how a dwi-mask will be generated.

[zafarneyaz]

I am also trying to create a new volume, suppose a brain tumor. then in surface mode, i want to show the tumor volume along with the labelled cortical surfaces. this may give surgeons a better orientation of mass lesion in relation to gyral anatomy.

Is there some way i can do this in brain suite

[Author]

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