Hi, Matthew,

I have just tried the cmd you gave me. After downloaded a few packages, it reported an error, the complete output message is below:

Solving environment: done

==> WARNING: A newer version of conda exists. <==

current version: 4.4.10

latest version: 4.5.1

Please update conda by running

$ conda update -n base conda

Downloading and Extracting Packages

jsoncpp 1.8.3: ######################################################### | 100%

sqlite 3.23.1: ######################################################### | 100%

graphite2 1.3.11: ###################################################### | 100%

pylint 1.8.2: ########################################################## | 100%

xz 5.2.3: ############################################################## | 100%

libxcb 1.13: ########################################################### | 100%

tornado 5.0.2: ######################################################### | 100%

psutil 5.4.5: ########################################################## | 100%

sortedcontainers 1.5.10: ############################################### | 100%

certifi 2018.4.16: ##################################################### | 100%

vtk 8.1.0: ############################################################# | 100%

pytz 2018.4: ########################################################### | 100%

pcre 8.42: ############################################################# | 100%

pexpect 4.5.0: ######################################################### | 100%

cytoolz 0.9.0.1: ####################################################### | 100%

decorator 4.3.0: ####################################################### | 100%

mkl 2018.0.2: ########################################################## | 100%

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):

File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda/exceptions.py", line 789, in __call__

return func(*args, **kwargs)

File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda_env/cli/main.py", line 74, in do_call

exit_code = getattr(module, func_name)(args, parser)

File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda_env/cli/main_create.py", line 108, in execute

installer.install(prefix, pkg_specs, args, env)

File "/usr/local/fsl/fslpython/lib/python3.6/site-packages/conda_env/installers/pip.py", line 36, in _pip_install_via_requirements

delete=False)

File "/usr/local/fsl/fslpython/lib/python3.6/tempfile.py", line 549, in NamedTemporaryFile

(fd, name) = _mkstemp_inner(dir, prefix, suffix, flags, output_type)

File "/usr/local/fsl/fslpython/lib/python3.6/tempfile.py", line 260, in _mkstemp_inner

fd = _os.open(file, flags, 0o600)

PermissionError: [Errno 13] Permission denied: '/usr/local/fsl/etc/fslconf/condaenv.bfuezlq6.requirements.txt'

`$ /usr/local/fsl/fslpython/bin/conda-env create -f /usr/local/fsl/etc/fslconf/fslpython_environment.yml`

environment variables:

ANTSPATH=/home/user/bin/ants/bin

CIO_TEST=<not set>

CLASSPATH=.:/usr/local/Java/jdk1.8.0_144/lib:/usr/local/Java/jdk1.8.0_144/jre/li

CONDA_ROOT=/usr/local/fsl/fslpython

DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path

LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64:

MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path

PATH=/home/user/anaconda3/bin:/usr/local/fsl/bin:/usr/local/Java/jdk1.8.0_144/bin:/usr/local/cuda-8

.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/u

sr/games:/usr/local/games:/snap/bin

REQUESTS_CA_BUNDLE=<not set>

SSL_CERT_FILE=<not set>

XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0

XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0

active environment : None

user config file : /home/user/.condarc

populated config files : /home/user/.condarc

conda version : 4.4.10

conda-build version : not installed

python version : 3.6.4.final.0

base environment : /usr/local/fsl/fslpython (read only)

channel URLs : https://conda.anaconda.org/conda-forge/linux-64

https://conda.anaconda.org/conda-forge/noarch

https://repo.continuum.io/pkgs/main/linux-64

https://repo.continuum.io/pkgs/main/noarch

https://repo.continuum.io/pkgs/free/linux-64

https://repo.continuum.io/pkgs/free/noarch

https://repo.continuum.io/pkgs/r/linux-64

https://repo.continuum.io/pkgs/r/noarch

https://repo.continuum.io/pkgs/pro/linux-64

https://repo.continuum.io/pkgs/pro/noarch

package cache : /usr/local/fsl/fslpython/pkgs

/home/user/.conda/pkgs

envs directories : /home/user/.conda/envs

/usr/local/fsl/fslpython/envs

platform : linux-64

user-agent : conda/4.4.10 requests/2.18.4 CPython/3.6.4 Linux/4.13.0-39-generic ubuntu/16.04 glibc/2.23

UID:GID : 1000:1000

netrc file : None

offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve

future releases of conda.

Would you like conda to send this report to the core maintainers?

[y/N]:

No report sent. To permanently opt-out, use

$ conda config --set report_errors false

I think there may have permission issue, so I ran the cmd again with sudo.

But,

CondaValueError: prefix already exists: /home/user/.conda/envs/fslpython

So, I found the "/home/user/.conda/envs/fslpython" directory, and delete the fslpython there.

I ran the cmd with sudo again. This time, program goes, with a warning says the directory '/home/user/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

Then the cmd goes on, downloaded some packages. Messages are:

Collecting SPARQLWrapper==1.7.6 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 1))

Downloading https://files.pythonhosted.org/packages/92/4f/e44f10d2d2a4c66c01f0f47e1aa1fe8addeedaf050e7cbcfa3a5ebce6f14/SPARQLWrapper-1.7.6.tar.gz

Collecting rdflib==4.2.1 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 2))

Downloading https://files.pythonhosted.org/packages/9d/fa/4198e8d8b444a4ace5c8fd86d128c2faa210a6e281973c8e5e16d978eaf4/rdflib-4.2.1.tar.gz (889kB)

100% |████████████████████████████████| 890kB 586kB/s

Collecting prov==1.4.0 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))

Downloading https://files.pythonhosted.org/packages/5a/fa/456e6ef4c936655e3fe8e60ec171eb064d3ea915b0db31ccced46314f765/prov-1.4.0-py2.py3-none-any.whl (242kB)

100% |████████████████████████████████| 245kB 768kB/s

Collecting nidmresults<2,>=1.1.0 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))

Downloading https://files.pythonhosted.org/packages/49/d5/fb65c1e9768ebddd5039fea6af0884d535d6ae95cc2c540ec2accdfb9310/nidmresults-1.2.1-py2.py3-none-any.whl (230kB)

100% |████████████████████████████████| 235kB 642kB/s

Collecting nidmfsl<2,>=1.1.0 (from -r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 5))

Downloading https://files.pythonhosted.org/packages/80/a5/b8cbdd8ff292eb29842c13b0aa5609709c61ad9f9dbd38486cd78bdbf447/nidmfsl-1.2.1-py2.py3-none-any.whl

Collecting keepalive>=0.5 (from SPARQLWrapper==1.7.6->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 1))

Downloading https://files.pythonhosted.org/packages/6a/11/8eaf21d74b06cfabd42ca9d2b7b216e071faa416753faeb3322f1863f585/keepalive-0.5.tar.gz

Requirement already satisfied: isodate in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from rdflib==4.2.1->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 2))

Requirement already satisfied: pyparsing in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from rdflib==4.2.1->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 2))

Requirement already satisfied: networkx>=1.10 in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))

Requirement already satisfied: six>=1.9.0 in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))

Requirement already satisfied: lxml in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))

Requirement already satisfied: python-dateutil in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))

Requirement already satisfied: nibabel in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))

Requirement already satisfied: numpy in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))

Requirement already satisfied: future in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))

Collecting rdflib-jsonld (from nidmresults<2,>=1.1.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 4))

Downloading https://files.pythonhosted.org/packages/ba/48/edaad22fc9de34500699f0c7fc9124385dd425fd18857244f126a6f7df66/rdflib-jsonld-0.4.0.tar.gz (53kB)

100% |████████████████████████████████| 61kB 1.1MB/s

Requirement already satisfied: decorator>=3.4.0 in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages (from networkx>=1.10->prov==1.4.0->-r /usr/local/fsl/etc/fslconf/condaenv.taout2k8.requirements.txt (line 3))

Installing collected packages: rdflib, keepalive, SPARQLWrapper, prov, rdflib-jsonld, nidmresults, nidmfsl

Running setup.py install for rdflib ... done

Running setup.py install for keepalive ... done

Running setup.py install for SPARQLWrapper ... done

Running setup.py install for rdflib-jsonld ... done

Successfully installed SPARQLWrapper-1.7.6 keepalive-0.5 nidmfsl-1.2.1 nidmresults-1.2.1 prov-1.4.0 rdflib-4.2.1 rdflib-jsonld-0.4.0

# To activate this environment, use:

# > source activate fslpython

# To deactivate an active environment, use:

# > source deactivate

I assume it is OK now?

So, I check the files under $FSLDIR/bin/ BUT there still not there. Instead, I found the '$FSLDIR/fslpython/envs/' now has a new directory fslpython.

And, in '$FSLDIR/fslpython/envs/fslpython/bin/', there are many files and I finally find the files missing:

ll im*

-rwxrwxr-x 1 root root 404 4月 28 15:07 imcp*

-rwxrwxr-x 1 root root 419 4月 28 15:07 img2png*

-rwxrwxr-x 1 root root 417 4月 28 15:07 img2py*

-rwxrwxr-x 1 root root 419 4月 28 15:07 img2xpm*

-rwxrwxr-x 1 root root 408 4月 28 15:07 imglob*

-rwxrwxr-x 1 root root 404 4月 28 15:07 immv*

But, seems this '$FSLDIR/fslpython/envs/fslpython/bin/' is not in the $PATH, and the terminal still says : 'imglob : command not found'

What to do next? Should I add this directory '$FSLDIR/fslpython/envs/fslpython/bin/' to PATH, OR should I just copy missing files to '$FSLDIR/bin/' ??