From pauldmccarthy at gmail.com  Wed Feb  8 08:55:11 2017
From: pauldmccarthy at gmail.com (paul mccarthy)
Date: Wed, 8 Feb 2017 13:55:11 +0000
Subject: [Neuroimaging] Thread-safe ArrayProxy/fileslice?
Message-ID: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>

Howdy all,

Does anybody have experience accessing image data through the ArrayProxy
class (or functions in the fileslice module) in a multi-threaded
environment? I am visualising large 4D images which are kept on disk (via
my indexed_gzip module), and am having trouble when accessing the data from
multiple threads, as the seek/read pairs from different threads will
occasionally become intertwined with each other.


My hacky workaround is to patch the ArrayProxy.__getitem__ method, and add
a threading.Lock to each instance, as follows:


import threading

import nibabel            as nib
import nibabel.arrayproxy as ap

def ArrayProxy__getitem__(self, slc):

    if not hasattr(self, '_thread_lock'):
        return self.__real_getitem__(slc)

    self._thread_lock.acquire()

    try:
        return ap.ArrayProxy.__real_getitem__(self, slc)

    finally:
        self._thread_lock.release()

# Patch ArrayProxy.__getitem__
ap.ArrayProxy.__real_getitem__ = ap.ArrayProxy.__getitem__
ap.ArrayProxy.__getitem__      = ArrayProxy__getitem__


# Then add a lock to instances
# which need to be thread-safe
img = nib.load('MNI152_T1_2mm.nii.gz')
img.dataobj._thread_lock = threading.Lock()


This is the first thing I came up with, although I will probably end up
adding the lock to the fileobj, and patching the fileslice.fileslice
function instead. Unless there are any better ideas?

Cheers,

Paul
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From effigies at bu.edu  Wed Feb  8 09:20:20 2017
From: effigies at bu.edu (Christopher Markiewicz)
Date: Wed, 8 Feb 2017 09:20:20 -0500
Subject: [Neuroimaging] Thread-safe ArrayProxy/fileslice?
In-Reply-To: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>
References: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>
Message-ID: <CAHE-diOHYnToMTEmnPXCkKJrzxiASCcZQgDfNQ9d_vdpcLQ6CQ@mail.gmail.com>

Is there any reason not to open a separate image object, per-thread? I'd
think that should keep the state sufficiently separated, though I would be
interested in the relative performance between that and your solution.

On Wed, Feb 8, 2017 at 8:55 AM, paul mccarthy <pauldmccarthy at gmail.com>
wrote:

> Howdy all,
>
> Does anybody have experience accessing image data through the ArrayProxy
> class (or functions in the fileslice module) in a multi-threaded
> environment? I am visualising large 4D images which are kept on disk (via
> my indexed_gzip module), and am having trouble when accessing the data
> from multiple threads, as the seek/read pairs from different threads will
> occasionally become intertwined with each other.
>
>
> My hacky workaround is to patch the ArrayProxy.__getitem__ method, and
> add a threading.Lock to each instance, as follows:
>
>
> import threading
>
> import nibabel            as nib
> import nibabel.arrayproxy as ap
>
> def ArrayProxy__getitem__(self, slc):
>
>     if not hasattr(self, '_thread_lock'):
>         return self.__real_getitem__(slc)
>
>     self._thread_lock.acquire()
>
>     try:
>         return ap.ArrayProxy.__real_getitem__(self, slc)
>
>     finally:
>         self._thread_lock.release()
>
> # Patch ArrayProxy.__getitem__
> ap.ArrayProxy.__real_getitem__ = ap.ArrayProxy.__getitem__
> ap.ArrayProxy.__getitem__      = ArrayProxy__getitem__
>
>
> # Then add a lock to instances
> # which need to be thread-safe
> img = nib.load('MNI152_T1_2mm.nii.gz')
> img.dataobj._thread_lock = threading.Lock()
>
>
> This is the first thing I came up with, although I will probably end up
> adding the lock to the fileobj, and patching the fileslice.fileslice
> function instead. Unless there are any better ideas?
>
> Cheers,
>
> Paul
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From pauldmccarthy at gmail.com  Wed Feb  8 10:48:10 2017
From: pauldmccarthy at gmail.com (paul mccarthy)
Date: Wed, 8 Feb 2017 15:48:10 +0000
Subject: [Neuroimaging] Thread-safe ArrayProxy/fileslice?
In-Reply-To: <CAHE-diOHYnToMTEmnPXCkKJrzxiASCcZQgDfNQ9d_vdpcLQ6CQ@mail.gmail.com>
References: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>
 <CAHE-diOHYnToMTEmnPXCkKJrzxiASCcZQgDfNQ9d_vdpcLQ6CQ@mail.gmail.com>
Message-ID: <CAD_xh8H05Z3zQtu4wyqRg1A-KbjmDRMG6uACu8LwvJQh2DmCtQ@mail.gmail.com>

Hi Christopher,

The way that indexed_gzip works, I'd prefer to only have a single file
object in existence - the file object creates an index allowing fast seeks
through the compressed data, and I don't want to have more than one index
created.

I've realised that I need to protect the individual paired calls to seek/
read in fileslice.read_segments (i.e. protect reading of each segment).
Protecting an entire call to read_segments blocks other threads
unacceptably long (e.g. I would like the user to be able to interact with
the current 3D volume while the 4D time series  for one or more voxels is
being read in).

So I will add a Lock object to my file objects, and monkey-patch
read_segments to use it.

Cheers,

Paul

On 8 February 2017 at 14:20, Christopher Markiewicz <effigies at bu.edu> wrote:

> Is there any reason not to open a separate image object, per-thread? I'd
> think that should keep the state sufficiently separated, though I would be
> interested in the relative performance between that and your solution.
>
> On Wed, Feb 8, 2017 at 8:55 AM, paul mccarthy <pauldmccarthy at gmail.com>
> wrote:
>
>> Howdy all,
>>
>> Does anybody have experience accessing image data through the ArrayProxy
>> class (or functions in the fileslice module) in a multi-threaded
>> environment? I am visualising large 4D images which are kept on disk (via
>> my indexed_gzip module), and am having trouble when accessing the data
>> from multiple threads, as the seek/read pairs from different threads
>> will occasionally become intertwined with each other.
>>
>>
>> My hacky workaround is to patch the ArrayProxy.__getitem__ method, and
>> add a threading.Lock to each instance, as follows:
>>
>>
>> import threading
>>
>> import nibabel            as nib
>> import nibabel.arrayproxy as ap
>>
>> def ArrayProxy__getitem__(self, slc):
>>
>>     if not hasattr(self, '_thread_lock'):
>>         return self.__real_getitem__(slc)
>>
>>     self._thread_lock.acquire()
>>
>>     try:
>>         return ap.ArrayProxy.__real_getitem__(self, slc)
>>
>>     finally:
>>         self._thread_lock.release()
>>
>> # Patch ArrayProxy.__getitem__
>> ap.ArrayProxy.__real_getitem__ = ap.ArrayProxy.__getitem__
>> ap.ArrayProxy.__getitem__      = ArrayProxy__getitem__
>>
>>
>> # Then add a lock to instances
>> # which need to be thread-safe
>> img = nib.load('MNI152_T1_2mm.nii.gz')
>> img.dataobj._thread_lock = threading.Lock()
>>
>>
>> This is the first thing I came up with, although I will probably end up
>> adding the lock to the fileobj, and patching the fileslice.fileslice
>> function instead. Unless there are any better ideas?
>>
>> Cheers,
>>
>> Paul
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From njs at pobox.com  Wed Feb  8 15:23:00 2017
From: njs at pobox.com (Nathaniel Smith)
Date: Wed, 8 Feb 2017 12:23:00 -0800
Subject: [Neuroimaging] Thread-safe ArrayProxy/fileslice?
In-Reply-To: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>
References: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>
Message-ID: <CAPJVwBm0JcYzW=L_FkOD=5J4Ff8BAwN5xBbf0SD5QoZaBtzbVw@mail.gmail.com>

The best solution would be to use a pread-style interface that lets you
read from a given offset without seeking at all, and thus without needing
any locks. Unfortunately, Python hasn't historically had the best support
for this, but it's available if you're using Python 3 on unix:
https://docs.python.org/3/library/os.html#os.pread

-n

On Feb 8, 2017 5:55 AM, "paul mccarthy" <pauldmccarthy at gmail.com> wrote:

> Howdy all,
>
> Does anybody have experience accessing image data through the ArrayProxy
> class (or functions in the fileslice module) in a multi-threaded
> environment? I am visualising large 4D images which are kept on disk (via
> my indexed_gzip module), and am having trouble when accessing the data
> from multiple threads, as the seek/read pairs from different threads will
> occasionally become intertwined with each other.
>
>
> My hacky workaround is to patch the ArrayProxy.__getitem__ method, and
> add a threading.Lock to each instance, as follows:
>
>
> import threading
>
> import nibabel            as nib
> import nibabel.arrayproxy as ap
>
> def ArrayProxy__getitem__(self, slc):
>
>     if not hasattr(self, '_thread_lock'):
>         return self.__real_getitem__(slc)
>
>     self._thread_lock.acquire()
>
>     try:
>         return ap.ArrayProxy.__real_getitem__(self, slc)
>
>     finally:
>         self._thread_lock.release()
>
> # Patch ArrayProxy.__getitem__
> ap.ArrayProxy.__real_getitem__ = ap.ArrayProxy.__getitem__
> ap.ArrayProxy.__getitem__      = ArrayProxy__getitem__
>
>
> # Then add a lock to instances
> # which need to be thread-safe
> img = nib.load('MNI152_T1_2mm.nii.gz')
> img.dataobj._thread_lock = threading.Lock()
>
>
> This is the first thing I came up with, although I will probably end up
> adding the lock to the fileobj, and patching the fileslice.fileslice
> function instead. Unless there are any better ideas?
>
> Cheers,
>
> Paul
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From pauldmccarthy at gmail.com  Wed Feb  8 16:12:25 2017
From: pauldmccarthy at gmail.com (paul mccarthy)
Date: Wed, 8 Feb 2017 21:12:25 +0000
Subject: [Neuroimaging] Thread-safe ArrayProxy/fileslice?
In-Reply-To: <CAPJVwBm0JcYzW=L_FkOD=5J4Ff8BAwN5xBbf0SD5QoZaBtzbVw@mail.gmail.com>
References: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>
 <CAPJVwBm0JcYzW=L_FkOD=5J4Ff8BAwN5xBbf0SD5QoZaBtzbVw@mail.gmail.com>
Message-ID: <CAD_xh8HeALQnyKbOtFhiAdH+_2rbvFzuk5zsYUQ6Sn59=Mg1mg@mail.gmail.com>

Hi Nathaniel,

True - perhaps such a method could be added to the Opener class (with the
internal seek/read calls protected by a mutex), and used by read_segments,
instead of separate seek/read calls. This would be a very simple change -
I'm happy to prepare a PR if it sounds like a good idea.

Cheers,

Paul

On 8 February 2017 at 20:23, Nathaniel Smith <njs at pobox.com> wrote:

> The best solution would be to use a pread-style interface that lets you
> read from a given offset without seeking at all, and thus without needing
> any locks. Unfortunately, Python hasn't historically had the best support
> for this, but it's available if you're using Python 3 on unix:
> https://docs.python.org/3/library/os.html#os.pread
>
> -n
>
> On Feb 8, 2017 5:55 AM, "paul mccarthy" <pauldmccarthy at gmail.com> wrote:
>
>> Howdy all,
>>
>> Does anybody have experience accessing image data through the ArrayProxy
>> class (or functions in the fileslice module) in a multi-threaded
>> environment? I am visualising large 4D images which are kept on disk (via
>> my indexed_gzip module), and am having trouble when accessing the data
>> from multiple threads, as the seek/read pairs from different threads
>> will occasionally become intertwined with each other.
>>
>>
>> My hacky workaround is to patch the ArrayProxy.__getitem__ method, and
>> add a threading.Lock to each instance, as follows:
>>
>>
>> import threading
>>
>> import nibabel            as nib
>> import nibabel.arrayproxy as ap
>>
>> def ArrayProxy__getitem__(self, slc):
>>
>>     if not hasattr(self, '_thread_lock'):
>>         return self.__real_getitem__(slc)
>>
>>     self._thread_lock.acquire()
>>
>>     try:
>>         return ap.ArrayProxy.__real_getitem__(self, slc)
>>
>>     finally:
>>         self._thread_lock.release()
>>
>> # Patch ArrayProxy.__getitem__
>> ap.ArrayProxy.__real_getitem__ = ap.ArrayProxy.__getitem__
>> ap.ArrayProxy.__getitem__      = ArrayProxy__getitem__
>>
>>
>> # Then add a lock to instances
>> # which need to be thread-safe
>> img = nib.load('MNI152_T1_2mm.nii.gz')
>> img.dataobj._thread_lock = threading.Lock()
>>
>>
>> This is the first thing I came up with, although I will probably end up
>> adding the lock to the fileobj, and patching the fileslice.fileslice
>> function instead. Unless there are any better ideas?
>>
>> Cheers,
>>
>> Paul
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From effigies at bu.edu  Wed Feb  8 16:18:57 2017
From: effigies at bu.edu (Christopher Markiewicz)
Date: Wed, 8 Feb 2017 16:18:57 -0500
Subject: [Neuroimaging] Thread-safe ArrayProxy/fileslice?
In-Reply-To: <CAD_xh8HeALQnyKbOtFhiAdH+_2rbvFzuk5zsYUQ6Sn59=Mg1mg@mail.gmail.com>
References: <CAD_xh8F1LsAaUzpoWCcbku-MU_jegafhfX7NhZCwrdkbqOsXWg@mail.gmail.com>
 <CAPJVwBm0JcYzW=L_FkOD=5J4Ff8BAwN5xBbf0SD5QoZaBtzbVw@mail.gmail.com>
 <CAD_xh8HeALQnyKbOtFhiAdH+_2rbvFzuk5zsYUQ6Sn59=Mg1mg@mail.gmail.com>
Message-ID: <CAHE-diMkWVD0N7=DyWz7vj0nioqd4E85vzMnvQ6sQ2DcENNyBQ@mail.gmail.com>

That sounds reasonable to me.

On Wed, Feb 8, 2017 at 4:12 PM, paul mccarthy <pauldmccarthy at gmail.com>
wrote:

> Hi Nathaniel,
>
> True - perhaps such a method could be added to the Opener class (with the
> internal seek/read calls protected by a mutex), and used by read_segments,
> instead of separate seek/read calls. This would be a very simple change -
> I'm happy to prepare a PR if it sounds like a good idea.
>
> Cheers,
>
> Paul
>
> On 8 February 2017 at 20:23, Nathaniel Smith <njs at pobox.com> wrote:
>
>> The best solution would be to use a pread-style interface that lets you
>> read from a given offset without seeking at all, and thus without needing
>> any locks. Unfortunately, Python hasn't historically had the best support
>> for this, but it's available if you're using Python 3 on unix:
>> https://docs.python.org/3/library/os.html#os.pread
>>
>> -n
>>
>> On Feb 8, 2017 5:55 AM, "paul mccarthy" <pauldmccarthy at gmail.com> wrote:
>>
>>> Howdy all,
>>>
>>> Does anybody have experience accessing image data through the ArrayProxy
>>> class (or functions in the fileslice module) in a multi-threaded
>>> environment? I am visualising large 4D images which are kept on disk (via
>>> my indexed_gzip module), and am having trouble when accessing the data
>>> from multiple threads, as the seek/read pairs from different threads
>>> will occasionally become intertwined with each other.
>>>
>>>
>>> My hacky workaround is to patch the ArrayProxy.__getitem__ method, and
>>> add a threading.Lock to each instance, as follows:
>>>
>>>
>>> import threading
>>>
>>> import nibabel            as nib
>>> import nibabel.arrayproxy as ap
>>>
>>> def ArrayProxy__getitem__(self, slc):
>>>
>>>     if not hasattr(self, '_thread_lock'):
>>>         return self.__real_getitem__(slc)
>>>
>>>     self._thread_lock.acquire()
>>>
>>>     try:
>>>         return ap.ArrayProxy.__real_getitem__(self, slc)
>>>
>>>     finally:
>>>         self._thread_lock.release()
>>>
>>> # Patch ArrayProxy.__getitem__
>>> ap.ArrayProxy.__real_getitem__ = ap.ArrayProxy.__getitem__
>>> ap.ArrayProxy.__getitem__      = ArrayProxy__getitem__
>>>
>>>
>>> # Then add a lock to instances
>>> # which need to be thread-safe
>>> img = nib.load('MNI152_T1_2mm.nii.gz')
>>> img.dataobj._thread_lock = threading.Lock()
>>>
>>>
>>> This is the first thing I came up with, although I will probably end up
>>> adding the lock to the fileobj, and patching the fileslice.fileslice
>>> function instead. Unless there are any better ideas?
>>>
>>> Cheers,
>>>
>>> Paul
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From spmanikam at gmail.com  Wed Feb  8 15:01:01 2017
From: spmanikam at gmail.com (Valliappan C A)
Date: Thu, 9 Feb 2017 01:31:01 +0530
Subject: [Neuroimaging] Seeking help in pysurfer installation
Message-ID: <CAO6dHF-sPtAcbUsVPY2P_CjzYJh-3Rex7J0Kc1ScHWE+U1y5bQ@mail.gmail.com>

Hello
I'm facing a problem while executing this command "*brain =
stc_mean.plot(hemi='lh', subjects_dir=subjects_dir)*" of the code link
<http://martinos.org/mne/dev/auto_examples/inverse/plot_label_from_stc.html#example-inverse-plot-label-from-stc-py>
.
the error that is displayed is :




















*The time_unit parameter default will change from 'ms' to 's' in MNE 0.14.
To avoid this warning specify the parameter explicitly.__main__:1:
DeprecationWarning: The time_unit parameter default will change from 'ms'
to 's' in MNE 0.14. To avoid this warning specify the parameter
explicitly.Traceback (most recent call last):  File
"<ipython-input-28-79c2c651899e>", line 1, in <module>    brain =
stc_mean.plot(hemi='lh', subjects_dir=subjects_dir)  File
"/home/prr/my_project/mne-python/mne/source_estimate.py", line 1334, in
plot    time_unit=time_unit)  File
"/home/prr/my_project/mne-python/mne/viz/_3d.py", line 784, in
plot_source_estimates    config_opts=config_opts)  File
"/home/prr/miniconda2/lib/python2.7/site-packages/surfer/viz.py", line 459,
in __init__    brain = _Hemisphere(subject_id, **kwargs)  File
"/home/prr/miniconda2/lib/python2.7/site-packages/surfer/viz.py", line
2511, in __init__    **geo_kwargs)TypeError: surfacefactory() argument
after ** must be a mapping, not unicode*

I have installed pysurfer and its dependencies as in the document. Imported
all the packages once to cross-verify and it worked. but still I'm getting
a error  can some one help me with this .
-- 
*Valliappan.C.A*
*BITS PILANI K K BIRLA GOA CAMPUS*
*Contact: +91-8378988093*
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From rosswilsonblair at gmail.com  Wed Feb  8 21:05:48 2017
From: rosswilsonblair at gmail.com (Ross Blair)
Date: Wed, 8 Feb 2017 18:05:48 -0800
Subject: [Neuroimaging] Seeking help in pysurfer installation
In-Reply-To: <CAO6dHF-sPtAcbUsVPY2P_CjzYJh-3Rex7J0Kc1ScHWE+U1y5bQ@mail.gmail.com>
References: <CAO6dHF-sPtAcbUsVPY2P_CjzYJh-3Rex7J0Kc1ScHWE+U1y5bQ@mail.gmail.com>
Message-ID: <CADSdQD=qPg3Xp2N=rhxG0LS3kditRsQ+VYq+phWZSu4YoEyoyw@mail.gmail.com>

D

On Feb 8, 2017 1:58 PM, "Valliappan C A" <spmanikam at gmail.com> wrote:

> Hello
> I'm facing a problem while executing this command "*brain =
> stc_mean.plot(hemi='lh', subjects_dir=subjects_dir)*" of the code link
> <http://martinos.org/mne/dev/auto_examples/inverse/plot_label_from_stc.html#example-inverse-plot-label-from-stc-py>
> .
> the error that is displayed is :
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *The time_unit parameter default will change from 'ms' to 's' in MNE 0.14.
> To avoid this warning specify the parameter explicitly.__main__:1:
> DeprecationWarning: The time_unit parameter default will change from 'ms'
> to 's' in MNE 0.14. To avoid this warning specify the parameter
> explicitly.Traceback (most recent call last):  File
> "<ipython-input-28-79c2c651899e>", line 1, in <module>    brain =
> stc_mean.plot(hemi='lh', subjects_dir=subjects_dir)  File
> "/home/prr/my_project/mne-python/mne/source_estimate.py", line 1334, in
> plot    time_unit=time_unit)  File
> "/home/prr/my_project/mne-python/mne/viz/_3d.py", line 784, in
> plot_source_estimates    config_opts=config_opts)  File
> "/home/prr/miniconda2/lib/python2.7/site-packages/surfer/viz.py", line 459,
> in __init__    brain = _Hemisphere(subject_id, **kwargs)  File
> "/home/prr/miniconda2/lib/python2.7/site-packages/surfer/viz.py", line
> 2511, in __init__    **geo_kwargs)TypeError: surfacefactory() argument
> after ** must be a mapping, not unicode*
>
> I have installed pysurfer and its dependencies as in the document.
> Imported all the packages once to cross-verify and it worked. but still I'm
> getting a error  can some one help me with this .
> --
> *Valliappan.C.A*
> *BITS PILANI K K BIRLA GOA CAMPUS*
> *Contact: +91-8378988093 <+91%2083789%2088093>*
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From alexandre.gramfort at telecom-paristech.fr  Thu Feb  9 03:06:34 2017
From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort)
Date: Thu, 9 Feb 2017 09:06:34 +0100
Subject: [Neuroimaging] Seeking help in pysurfer installation
In-Reply-To: <CAO6dHF-sPtAcbUsVPY2P_CjzYJh-3Rex7J0Kc1ScHWE+U1y5bQ@mail.gmail.com>
References: <CAO6dHF-sPtAcbUsVPY2P_CjzYJh-3Rex7J0Kc1ScHWE+U1y5bQ@mail.gmail.com>
Message-ID: <CADeotZpeow9_c7P1xTpdP-wR6Zg5NXFdhcGGjE5A+CwjXAouDw@mail.gmail.com>

hi,

you should post this as an issue on the MNE issue tracker on github.

It can be a mismatch between the pysurfer version and mne-python.

Alex


On Wed, Feb 8, 2017 at 9:01 PM, Valliappan C A <spmanikam at gmail.com> wrote:
> Hello
> I'm facing a problem while executing this command "brain =
> stc_mean.plot(hemi='lh', subjects_dir=subjects_dir)" of the code link .
> the error that is displayed is :
>
> The time_unit parameter default will change from 'ms' to 's' in MNE 0.14. To
> avoid this warning specify the parameter explicitly.
> __main__:1: DeprecationWarning: The time_unit parameter default will change
> from 'ms' to 's' in MNE 0.14. To avoid this warning specify the parameter
> explicitly.
> Traceback (most recent call last):
>
>   File "<ipython-input-28-79c2c651899e>", line 1, in <module>
>     brain = stc_mean.plot(hemi='lh', subjects_dir=subjects_dir)
>
>   File "/home/prr/my_project/mne-python/mne/source_estimate.py", line 1334,
> in plot
>     time_unit=time_unit)
>
>   File "/home/prr/my_project/mne-python/mne/viz/_3d.py", line 784, in
> plot_source_estimates
>     config_opts=config_opts)
>
>   File "/home/prr/miniconda2/lib/python2.7/site-packages/surfer/viz.py",
> line 459, in __init__
>     brain = _Hemisphere(subject_id, **kwargs)
>
>   File "/home/prr/miniconda2/lib/python2.7/site-packages/surfer/viz.py",
> line 2511, in __init__
>     **geo_kwargs)
>
> TypeError: surfacefactory() argument after ** must be a mapping, not unicode
>
> I have installed pysurfer and its dependencies as in the document. Imported
> all the packages once to cross-verify and it worked. but still I'm getting a
> error  can some one help me with this .
> --
> Valliappan.C.A
> BITS PILANI K K BIRLA GOA CAMPUS
> Contact: +91-8378988093
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>

From matthew.brett at gmail.com  Sat Feb 11 04:45:06 2017
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sat, 11 Feb 2017 09:45:06 +0000
Subject: [Neuroimaging] Nipy bugfix release
Message-ID: <CAH6Pt5qu50A-COZYpz-9=Eo4eNXQdH1jsRvVK++=NGm-Ed-DHw@mail.gmail.com>

Hi,

I just released nipy 0.4.1.   I've appended the Changelog entry, but
the release is primarily to make nipy compatible with Python 3.6,
Numpy 1.12, Sympy 1.0.

Many thanks to:

Matteo Visconti dOC
Yaroslav Halchenko
Lilian Besson
Horea Christian
Bertrand Thirion
Joke Durnez
Igor Gnatenko
Virgile Fritsch

for your contributions.

As usual

    pip install --user --upgrade nipy

Happy Nipying,

Matthew

Changelog
--------------

  Bugfix, refactoring and compatibility release.

  * New discrete cosine transform functions for building basis sets;
  * Fixes for compatibility with Python 3.6;
  * Fixes for compatibility with Numpy 1.12 (1.12 no longer allows
floating point values for indexing and other places where an integer
value is required);
  * Fixes for compatibility with Sympy 1.0;
  * Drop compatibility with Python 2.6, 3.2, 3.3;
  * Add ability to pass plotting arguments to ``plot_anat`` function
(Matteo Visconti dOC);
  * Some helpers for working with OpenFMRI datasets;
  * Signal upcoming change in return shape from ``make_recarray`` when
passing in an array for values. Allow user to select upcoming behavior
with keyword argument;
  * Bug fix for axis selection when using record arrays in numpies <= 1.7.1;
  * Add flag to allow SpaceTimeRealign to read TR from image headers
(Horea Christian).

From arokem at gmail.com  Sat Feb 11 13:58:43 2017
From: arokem at gmail.com (Ariel Rokem)
Date: Sat, 11 Feb 2017 10:58:43 -0800
Subject: [Neuroimaging] Nipy bugfix release
In-Reply-To: <CAH6Pt5qu50A-COZYpz-9=Eo4eNXQdH1jsRvVK++=NGm-Ed-DHw@mail.gmail.com>
References: <CAH6Pt5qu50A-COZYpz-9=Eo4eNXQdH1jsRvVK++=NGm-Ed-DHw@mail.gmail.com>
Message-ID: <CA+X4w0w0to0+N9_WAzVB67sOGD5HrD_NG8-pW5PX_O1H0XkZSg@mail.gmail.com>

Hooray! Nipy keeps nipying on!

On Sat, Feb 11, 2017 at 1:45 AM, Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> I just released nipy 0.4.1.   I've appended the Changelog entry, but
> the release is primarily to make nipy compatible with Python 3.6,
> Numpy 1.12, Sympy 1.0.
>
>
Could you please point me to the PRs relevant to Python 3.6 compatibility?
I am curious to see what you did there.

Thanks!

Ariel



> Many thanks to:
>
> Matteo Visconti dOC
> Yaroslav Halchenko
> Lilian Besson
> Horea Christian
> Bertrand Thirion
> Joke Durnez
> Igor Gnatenko
> Virgile Fritsch
>
> for your contributions.
>
> As usual
>
>     pip install --user --upgrade nipy
>
> Happy Nipying,
>
> Matthew
>
> Changelog
> --------------
>
>   Bugfix, refactoring and compatibility release.
>
>   * New discrete cosine transform functions for building basis sets;
>   * Fixes for compatibility with Python 3.6;
>   * Fixes for compatibility with Numpy 1.12 (1.12 no longer allows
> floating point values for indexing and other places where an integer
> value is required);
>   * Fixes for compatibility with Sympy 1.0;
>   * Drop compatibility with Python 2.6, 3.2, 3.3;
>   * Add ability to pass plotting arguments to ``plot_anat`` function
> (Matteo Visconti dOC);
>   * Some helpers for working with OpenFMRI datasets;
>   * Signal upcoming change in return shape from ``make_recarray`` when
> passing in an array for values. Allow user to select upcoming behavior
> with keyword argument;
>   * Bug fix for axis selection when using record arrays in numpies <=
> 1.7.1;
>   * Add flag to allow SpaceTimeRealign to read TR from image headers
> (Horea Christian).
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From elef at indiana.edu  Wed Feb 15 19:15:33 2017
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Thu, 16 Feb 2017 00:15:33 +0000
Subject: [Neuroimaging]  [DIPY] Re-igniting our awesome developer meetings
Message-ID: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>

Hi all,

It has been some time from the last time we had a developers meeting. And I
think we really need
to improve our coordination across the different sites. Thanks all for
helping with the transition.

Also apologies for not being so much active in github. As expected,
starting a lab and teaching can bring
some delays.

So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
should be okay for all the main DIPY centers (Asia, Europe, America).
If you cannot attend then I 'll be happy to create a doodle.

Here are some ideas for the agenda:

- Releasing 12. Tomorrow will send a list of final PRs for the release.
- Web transition. We have new website let's start using it.
- GSoC mentors for 2017. I have already started a wiki
https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
- OHBM, MICCAI and Brainhack participations.
- Other urgent topics. Compilation issues etc.

I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
Stephen. Of course the rest can join too.

So, we should try to have a similar meeting once a month. And scientific
hangouts once every 2 months.
Let me know if you think otherwise.

Crack on! 0.12 on the way! :)

Best regards,
Eleftherios
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From arokem at gmail.com  Wed Feb 15 23:04:17 2017
From: arokem at gmail.com (Ariel Rokem)
Date: Wed, 15 Feb 2017 20:04:17 -0800
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
Message-ID: <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>

On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

> Hi all,
>
> It has been some time from the last time we had a developers meeting. And
> I think we really need
> to improve our coordination across the different sites. Thanks all for
> helping with the transition.
>
> Also apologies for not being so much active in github. As expected,
> starting a lab and teaching can bring
> some delays.
>
> So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
> should be okay for all the main DIPY centers (Asia, Europe, America).
> If you cannot attend then I 'll be happy to create a doodle.
>
> Here are some ideas for the agenda:
>
> - Releasing 12. Tomorrow will send a list of final PRs for the release.
> - Web transition. We have new website let's start using it.
> - GSoC mentors for 2017. I have already started a wiki
> https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
> - OHBM, MICCAI and Brainhack participations.
> - Other urgent topics. Compilation issues etc.
>
> I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
> Stephen. Of course the rest can join too.
>
>
I'll be there.

Ariel


> So, we should try to have a similar meeting once a month. And scientific
> hangouts once every 2 months.
> Let me know if you think otherwise.
>
> Crack on! 0.12 on the way! :)
>
> Best regards,
> Eleftherios
>
>
>
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From skab12 at gmail.com  Thu Feb 16 07:33:46 2017
From: skab12 at gmail.com (K. Serge)
Date: Thu, 16 Feb 2017 13:33:46 +0100
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
 <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
Message-ID: <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>

Unfortunatly, i can't.

Serge

ps: In general, wednesday is complicated for me.



2017-02-16 5:04 GMT+01:00 Ariel Rokem <arokem at gmail.com>:

>
>
> On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <
> elef at indiana.edu> wrote:
>
>> Hi all,
>>
>> It has been some time from the last time we had a developers meeting. And
>> I think we really need
>> to improve our coordination across the different sites. Thanks all for
>> helping with the transition.
>>
>> Also apologies for not being so much active in github. As expected,
>> starting a lab and teaching can bring
>> some delays.
>>
>> So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
>> should be okay for all the main DIPY centers (Asia, Europe, America).
>> If you cannot attend then I 'll be happy to create a doodle.
>>
>> Here are some ideas for the agenda:
>>
>> - Releasing 12. Tomorrow will send a list of final PRs for the release.
>> - Web transition. We have new website let's start using it.
>> - GSoC mentors for 2017. I have already started a wiki
>> https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
>> - OHBM, MICCAI and Brainhack participations.
>> - Other urgent topics. Compilation issues etc.
>>
>> I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
>> Stephen. Of course the rest can join too.
>>
>>
> I'll be there.
>
> Ariel
>
>
>> So, we should try to have a similar meeting once a month. And scientific
>> hangouts once every 2 months.
>> Let me know if you think otherwise.
>>
>> Crack on! 0.12 on the way! :)
>>
>> Best regards,
>> Eleftherios
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
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From skab12 at gmail.com  Thu Feb 16 12:10:30 2017
From: skab12 at gmail.com (K. Serge)
Date: Thu, 16 Feb 2017 18:10:30 +0100
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
 <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
 <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>
Message-ID: <CACydq8oV+o4Q0TBV9jMK-8fk-e1ShCDQyiSFUArzD91zf+eFsg@mail.gmail.com>

Sorry, I mixed the date. I'll be there

Serge K.

2017-02-16 13:33 GMT+01:00 K. Serge <skab12 at gmail.com>:

> Unfortunatly, i can't.
>
> Serge
>
> ps: In general, wednesday is complicated for me.
>
>
>
> 2017-02-16 5:04 GMT+01:00 Ariel Rokem <arokem at gmail.com>:
>
>>
>>
>> On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <
>> elef at indiana.edu> wrote:
>>
>>> Hi all,
>>>
>>> It has been some time from the last time we had a developers meeting.
>>> And I think we really need
>>> to improve our coordination across the different sites. Thanks all for
>>> helping with the transition.
>>>
>>> Also apologies for not being so much active in github. As expected,
>>> starting a lab and teaching can bring
>>> some delays.
>>>
>>> So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
>>> should be okay for all the main DIPY centers (Asia, Europe, America).
>>> If you cannot attend then I 'll be happy to create a doodle.
>>>
>>> Here are some ideas for the agenda:
>>>
>>> - Releasing 12. Tomorrow will send a list of final PRs for the release.
>>> - Web transition. We have new website let's start using it.
>>> - GSoC mentors for 2017. I have already started a wiki
>>> https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
>>> - OHBM, MICCAI and Brainhack participations.
>>> - Other urgent topics. Compilation issues etc.
>>>
>>> I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
>>> Stephen. Of course the rest can join too.
>>>
>>>
>> I'll be there.
>>
>> Ariel
>>
>>
>>> So, we should try to have a similar meeting once a month. And scientific
>>> hangouts once every 2 months.
>>> Let me know if you think otherwise.
>>>
>>> Crack on! 0.12 on the way! :)
>>>
>>> Best regards,
>>> Eleftherios
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>
>
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From stephan.meesters at gmail.com  Thu Feb 16 12:30:45 2017
From: stephan.meesters at gmail.com (Stephan Meesters)
Date: Thu, 16 Feb 2017 17:30:45 +0000
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CACydq8oV+o4Q0TBV9jMK-8fk-e1ShCDQyiSFUArzD91zf+eFsg@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
 <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
 <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>
 <CACydq8oV+o4Q0TBV9jMK-8fk-e1ShCDQyiSFUArzD91zf+eFsg@mail.gmail.com>
Message-ID: <CAKLc09+wF7dx2K-s-_U7yvzRvEa1VPgkzP01Wg81Vrhye61PbQ@mail.gmail.com>

Hi Eleftherios

Sorry but it's not at a very convenient time for me (5 am). I don't think
my brain functions at this time of day =)

In any case I will be able to meet up at the ISMRM this year, but not at
OHBM unfortunately. Maybe MICCAI.

Regards Stephan

On Thu, 16 Feb 2017 at 18:10, K. Serge <skab12 at gmail.com> wrote:

Sorry, I mixed the date. I'll be there

Serge K.

2017-02-16 13:33 GMT+01:00 K. Serge <skab12 at gmail.com>:

Unfortunatly, i can't.

Serge

ps: In general, wednesday is complicated for me.



2017-02-16 5:04 GMT+01:00 Ariel Rokem <arokem at gmail.com>:



On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

Hi all,

It has been some time from the last time we had a developers meeting. And I
think we really need
to improve our coordination across the different sites. Thanks all for
helping with the transition.

Also apologies for not being so much active in github. As expected,
starting a lab and teaching can bring
some delays.

So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
should be okay for all the main DIPY centers (Asia, Europe, America).
If you cannot attend then I 'll be happy to create a doodle.

Here are some ideas for the agenda:

- Releasing 12. Tomorrow will send a list of final PRs for the release.
- Web transition. We have new website let's start using it.
- GSoC mentors for 2017. I have already started a wiki
https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
- OHBM, MICCAI and Brainhack participations.
- Other urgent topics. Compilation issues etc.

I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
Stephen. Of course the rest can join too.


I'll be there.

Ariel


So, we should try to have a similar meeting once a month. And scientific
hangouts once every 2 months.
Let me know if you think otherwise.

Crack on! 0.12 on the way! :)

Best regards,
Eleftherios






_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org
https://mail.python.org/mailman/listinfo/neuroimaging
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From elef at indiana.edu  Thu Feb 16 12:52:50 2017
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Thu, 16 Feb 2017 17:52:50 +0000
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CAKLc09+wF7dx2K-s-_U7yvzRvEa1VPgkzP01Wg81Vrhye61PbQ@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
 <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
 <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>
 <CACydq8oV+o4Q0TBV9jMK-8fk-e1ShCDQyiSFUArzD91zf+eFsg@mail.gmail.com>
 <CAKLc09+wF7dx2K-s-_U7yvzRvEa1VPgkzP01Wg81Vrhye61PbQ@mail.gmail.com>
Message-ID: <CAN6JmWOh6N4dnXRdG_34ngx8u6DOjsG7vnTXxcNDbWecuRE5Ow@mail.gmail.com>

Wait we can change the time. I didn't realize that it will be so early in
Europe. My bad! Let me share a doodle!
We may have the problem now that it maybe too early/late in Asia.

Here is the link!

http://doodle.com/poll/c2qiayevwczh9e24

Best,
Eleftherios



On Thu, Feb 16, 2017 at 12:42 PM Stephan Meesters <
stephan.meesters at gmail.com> wrote:

> Hi Eleftherios
>
> Sorry but it's not at a very convenient time for me (5 am). I don't think
> my brain functions at this time of day =)
>
> In any case I will be able to meet up at the ISMRM this year, but not at
> OHBM unfortunately. Maybe MICCAI.
>
> Regards Stephan
>
> On Thu, 16 Feb 2017 at 18:10, K. Serge <skab12 at gmail.com> wrote:
>
> Sorry, I mixed the date. I'll be there
>
> Serge K.
>
> 2017-02-16 13:33 GMT+01:00 K. Serge <skab12 at gmail.com>:
>
> Unfortunatly, i can't.
>
> Serge
>
> ps: In general, wednesday is complicated for me.
>
>
>
> 2017-02-16 5:04 GMT+01:00 Ariel Rokem <arokem at gmail.com>:
>
>
>
> On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <
> elef at indiana.edu> wrote:
>
> Hi all,
>
> It has been some time from the last time we had a developers meeting. And
> I think we really need
> to improve our coordination across the different sites. Thanks all for
> helping with the transition.
>
> Also apologies for not being so much active in github. As expected,
> starting a lab and teaching can bring
> some delays.
>
> So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
> should be okay for all the main DIPY centers (Asia, Europe, America).
> If you cannot attend then I 'll be happy to create a doodle.
>
> Here are some ideas for the agenda:
>
> - Releasing 12. Tomorrow will send a list of final PRs for the release.
> - Web transition. We have new website let's start using it.
> - GSoC mentors for 2017. I have already started a wiki
> https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
> - OHBM, MICCAI and Brainhack participations.
> - Other urgent topics. Compilation issues etc.
>
> I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
> Stephen. Of course the rest can join too.
>
>
> I'll be there.
>
> Ariel
>
>
> So, we should try to have a similar meeting once a month. And scientific
> hangouts once every 2 months.
> Let me know if you think otherwise.
>
> Crack on! 0.12 on the way! :)
>
> Best regards,
> Eleftherios
>
>
>
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From arokem at gmail.com  Fri Feb 17 00:23:30 2017
From: arokem at gmail.com (Ariel Rokem)
Date: Thu, 16 Feb 2017 21:23:30 -0800
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CAN6JmWOh6N4dnXRdG_34ngx8u6DOjsG7vnTXxcNDbWecuRE5Ow@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
 <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
 <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>
 <CACydq8oV+o4Q0TBV9jMK-8fk-e1ShCDQyiSFUArzD91zf+eFsg@mail.gmail.com>
 <CAKLc09+wF7dx2K-s-_U7yvzRvEa1VPgkzP01Wg81Vrhye61PbQ@mail.gmail.com>
 <CAN6JmWOh6N4dnXRdG_34ngx8u6DOjsG7vnTXxcNDbWecuRE5Ow@mail.gmail.com>
Message-ID: <CA+X4w0xKj59QoWbA7AZhUHnkTZ_n_XJhPH-OM5r92pZYBgDYTg@mail.gmail.com>

On Thu, Feb 16, 2017 at 9:52 AM, Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

> Wait we can change the time. I didn't realize that it will be so early in
> Europe. My bad! Let me share a doodle!
> We may have the problem now that it maybe too early/late in Asia.
>
> Here is the link!
>
> http://doodle.com/poll/c2qiayevwczh9e24
>
>
Sorry - I can't make any of these times. If you could please take notes, we
can follow up here asynchronously after you have that discussion.


> Best,
> Eleftherios
>
>
>
> On Thu, Feb 16, 2017 at 12:42 PM Stephan Meesters <
> stephan.meesters at gmail.com> wrote:
>
>> Hi Eleftherios
>>
>> Sorry but it's not at a very convenient time for me (5 am). I don't think
>> my brain functions at this time of day =)
>>
>> In any case I will be able to meet up at the ISMRM this year, but not at
>> OHBM unfortunately. Maybe MICCAI.
>>
>> Regards Stephan
>>
>> On Thu, 16 Feb 2017 at 18:10, K. Serge <skab12 at gmail.com> wrote:
>>
>> Sorry, I mixed the date. I'll be there
>>
>> Serge K.
>>
>> 2017-02-16 13:33 GMT+01:00 K. Serge <skab12 at gmail.com>:
>>
>> Unfortunatly, i can't.
>>
>> Serge
>>
>> ps: In general, wednesday is complicated for me.
>>
>>
>>
>> 2017-02-16 5:04 GMT+01:00 Ariel Rokem <arokem at gmail.com>:
>>
>>
>>
>> On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <
>> elef at indiana.edu> wrote:
>>
>> Hi all,
>>
>> It has been some time from the last time we had a developers meeting. And
>> I think we really need
>> to improve our coordination across the different sites. Thanks all for
>> helping with the transition.
>>
>> Also apologies for not being so much active in github. As expected,
>> starting a lab and teaching can bring
>> some delays.
>>
>> So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
>> should be okay for all the main DIPY centers (Asia, Europe, America).
>> If you cannot attend then I 'll be happy to create a doodle.
>>
>> Here are some ideas for the agenda:
>>
>> - Releasing 12. Tomorrow will send a list of final PRs for the release.
>> - Web transition. We have new website let's start using it.
>> - GSoC mentors for 2017. I have already started a wiki
>> https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
>> - OHBM, MICCAI and Brainhack participations.
>> - Other urgent topics. Compilation issues etc.
>>
>> I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
>> Stephen. Of course the rest can join too.
>>
>>
>> I'll be there.
>>
>> Ariel
>>
>>
>> So, we should try to have a similar meeting once a month. And scientific
>> hangouts once every 2 months.
>> Let me know if you think otherwise.
>>
>> Crack on! 0.12 on the way! :)
>>
>> Best regards,
>> Eleftherios
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
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From arokem at gmail.com  Sat Feb 18 13:08:12 2017
From: arokem at gmail.com (Ariel Rokem)
Date: Sat, 18 Feb 2017 10:08:12 -0800
Subject: [Neuroimaging] Neurohackweek 2017: a summer school in human
 neuroscience and data science, September 4th-8th
Message-ID: <CA+X4w0wKnpWCMXRz3HV8v=mTZKpCppcB5yxUq12hPxcWh2Roug@mail.gmail.com>

We are happy to announce a call for applications to participate in the
Neurohackweek summer school for neuroimaging and data science.


This 5 day hands-on workshop, held at the University of Washington eScience
Institute in Seattle, will focus on technologies used to analyze human
neuroscience data, on methods used to extract information from large
datasets of publicly available data (such as the Human Connectome Project,
OpenfMRI, etc.), and on tools for making human neuroscience research open
and reproducible.


Morning sessions will be devoted to lectures and tutorials, and afternoon
sessions will be devoted to participant-directed activities: guided work on
team projects, hackathon sessions, and breakout sessions on topics of
interest.


For more details, see: http://neurohackweek.github.io/


We are now accepting applications from trainees and researchers in
different stages of their career (graduate students, postdocs, faculty, and
research staff) to participate at:


https://form.jotformeu.com/70342294106348


Some experience in human neuroscience and at least basic knowledge in
programming is desired, but we welcome applications from participants with
a variety of relevant backgrounds.


Accepted applicants will be asked to pay a fee of $200 upon final
registration. This fee will include participation in the course,
accommodation in the UW dorms, and two meals a day (breakfast and lunch),
for the duration of the course. A limited number of fee waivers and travel
grants will be available. We encourage students with financial need and
students from groups that are underrepresented in neuroimaging and data
science to apply for these grants (see application form for details).


*Important dates:*


April 18th: Deadline for applications to participate

May 6th: Notification of acceptance

June 1st: Final registration deadline


On behalf of the instructors,


Ariel Rokem, UW eScience

Tal Yarkoni, UT Austin
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From gael.varoquaux at normalesup.org  Tue Feb 21 07:57:28 2017
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Tue, 21 Feb 2017 13:57:28 +0100
Subject: [Neuroimaging] Bug in reading freesurfer annotation in nibabel?
Message-ID: <20170221125728.GB3590983@phare.normalesup.org>

Hi,

I am trying to load the freesurfer Destrieux atlas annotation file:
right.aparc.a2009s.annot
and I get the following error:

In [2]: import nibabel as nb

In [3]:
nb.freesurfer.read_annot('/home/varoquau/nilearn_data/destrieux_surface/left.aparc.a2009s.annot')
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call
last)
<ipython-input-3-610fc2be58c1> in <module>()
----> 1
nb.freesurfer.read_annot('/home/varoquau/nilearn_data/destrieux_surface/left.aparc.a2009s.annot')

/home/varoquau/dev/nibabel/nibabel/freesurfer/io.pyc in
read_annot(filepath, orig_ids)
    320     with open(filepath, "rb") as fobj:
    321         dt = ">i4"
--> 322         vnum = np.fromfile(fobj, dt, 1)[0]
    323         data = np.fromfile(fobj, dt, vnum * 2).reshape(vnum, 2)
    324         labels = data[:, 1]

IndexError: index 0 is out of bounds for axis 0 with size 0

Same failure for the right annotation (with nibabel 2.1 or master).

Am I doing something wrong (eg file corrupted) or are people having the
same problem? This is a naive question: I know nothing about surfaces.

Cheers,

Ga?l

-- 
    Gael Varoquaux
    Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux

From satra at mit.edu  Tue Feb 21 08:11:39 2017
From: satra at mit.edu (Satrajit Ghosh)
Date: Tue, 21 Feb 2017 08:11:39 -0500
Subject: [Neuroimaging] Bug in reading freesurfer annotation in nibabel?
In-Reply-To: <20170221125728.GB3590983@phare.normalesup.org>
References: <20170221125728.GB3590983@phare.normalesup.org>
Message-ID: <CA+A4wOngvgKm7u57EyT2QRuT5WrAE6sCBdpw=mrjAsHPiP6b8Q@mail.gmail.com>

hi gael,

seems like a corrupted file. with the same routine i read an annot a2005s,
and two different a2009s from recent data.

the annot files store indexed values aligned with the surfaces (e.g.,
lh.pial, lh.white) and in addition can store a color table. the annot value
itself is an rgb that's bit combined into an integer.

details here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotationfile

cheers,

satra

On Tue, Feb 21, 2017 at 7:57 AM, Gael Varoquaux <
gael.varoquaux at normalesup.org> wrote:

> Hi,
>
> I am trying to load the freesurfer Destrieux atlas annotation file:
> right.aparc.a2009s.annot
> and I get the following error:
>
> In [2]: import nibabel as nb
>
> In [3]:
> nb.freesurfer.read_annot('/home/varoquau/nilearn_data/
> destrieux_surface/left.aparc.a2009s.annot')
> ------------------------------------------------------------
> ---------------
> IndexError                                Traceback (most recent call
> last)
> <ipython-input-3-610fc2be58c1> in <module>()
> ----> 1
> nb.freesurfer.read_annot('/home/varoquau/nilearn_data/
> destrieux_surface/left.aparc.a2009s.annot')
>
> /home/varoquau/dev/nibabel/nibabel/freesurfer/io.pyc in
> read_annot(filepath, orig_ids)
>     320     with open(filepath, "rb") as fobj:
>     321         dt = ">i4"
> --> 322         vnum = np.fromfile(fobj, dt, 1)[0]
>     323         data = np.fromfile(fobj, dt, vnum * 2).reshape(vnum, 2)
>     324         labels = data[:, 1]
>
> IndexError: index 0 is out of bounds for axis 0 with size 0
>
> Same failure for the right annotation (with nibabel 2.1 or master).
>
> Am I doing something wrong (eg file corrupted) or are people having the
> same problem? This is a naive question: I know nothing about surfaces.
>
> Cheers,
>
> Ga?l
>
> --
>     Gael Varoquaux
>     Researcher, INRIA Parietal
>     NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
>     Phone:  ++ 33-1-69-08-79-68
>     http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From satra at mit.edu  Tue Feb 21 08:20:14 2017
From: satra at mit.edu (Satrajit Ghosh)
Date: Tue, 21 Feb 2017 08:20:14 -0500
Subject: [Neuroimaging] Nipype Workshop and Hackweek at MIT, March 27-31,
 2017
Message-ID: <CA+A4wOkBhCEEY5tXRDFHoxBk-RK8bAxPwJD4HRDW9HYC0g2J6g@mail.gmail.com>

The Nipype development team will be holding a workshop and hackweek at MIT,
Cambridge, MA, USA, from March 27 - 31.

For details and registration see: http://nipy.org/workshops/
2017-03-boston/index.html

cheers,

satra
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From gael.varoquaux at normalesup.org  Tue Feb 21 11:31:56 2017
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Tue, 21 Feb 2017 17:31:56 +0100
Subject: [Neuroimaging] Bug in reading freesurfer annotation in nibabel?
In-Reply-To: <CA+A4wOngvgKm7u57EyT2QRuT5WrAE6sCBdpw=mrjAsHPiP6b8Q@mail.gmail.com>
References: <20170221125728.GB3590983@phare.normalesup.org>
 <CA+A4wOngvgKm7u57EyT2QRuT5WrAE6sCBdpw=mrjAsHPiP6b8Q@mail.gmail.com>
Message-ID: <20170221163156.GB3673952@phare.normalesup.org>

Thanks for the info, Satra, it's probably a problem with the file. We are
investigating.

G

On Tue, Feb 21, 2017 at 08:11:39AM -0500, Satrajit Ghosh wrote:
> hi gael,

> seems like a corrupted file. with the same routine i read an annot a2005s, and
> two different a2009s from recent data.

> the annot files store indexed values aligned with the surfaces (e.g., lh.pial,
> lh.white) and in addition can store a color table. the annot value itself is an
> rgb that's bit combined into an integer.

> details here: https://surfer.nmr.mgh.harvard.edu/fswiki/
> LabelsClutsAnnotationFiles#Annotationfile

> cheers,

> satra

> On Tue, Feb 21, 2017 at 7:57 AM, Gael Varoquaux <gael.varoquaux at normalesup.org>
> wrote:

>     Hi,

>     I am trying to load the freesurfer Destrieux atlas annotation file:
>     right.aparc.a2009s.annot
>     and I get the following error:

>     In [2]: import nibabel as nb

>     In [3]:
>     nb.freesurfer.read_annot('/home/varoquau/nilearn_data/destrieux_surface/
>     left.aparc.a2009s.annot')
>     ---------------------------------------------------------------------------
>     IndexError? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Traceback (most recent call
>     last)
>     <ipython-input-3-610fc2be58c1> in <module>()
>     ----> 1
>     nb.freesurfer.read_annot('/home/varoquau/nilearn_data/destrieux_surface/
>     left.aparc.a2009s.annot')

>     /home/varoquau/dev/nibabel/nibabel/freesurfer/io.pyc in
>     read_annot(filepath, orig_ids)
>     ? ? 320? ? ?with open(filepath, "rb") as fobj:
>     ? ? 321? ? ? ? ?dt = ">i4"
>     --> 322? ? ? ? ?vnum = np.fromfile(fobj, dt, 1)[0]
>     ? ? 323? ? ? ? ?data = np.fromfile(fobj, dt, vnum * 2).reshape(vnum, 2)
>     ? ? 324? ? ? ? ?labels = data[:, 1]

>     IndexError: index 0 is out of bounds for axis 0 with size 0

>     Same failure for the right annotation (with nibabel 2.1 or master).

>     Am I doing something wrong (eg file corrupted) or are people having the
>     same problem? This is a naive question: I know nothing about surfaces.

>     Cheers,

>     Ga?l
-- 
    Gael Varoquaux
    Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux

From valeriehayot at gmail.com  Wed Feb 22 14:22:26 2017
From: valeriehayot at gmail.com (val hs)
Date: Wed, 22 Feb 2017 14:22:26 -0500
Subject: [Neuroimaging] Reading a byte stream into nibabel
Message-ID: <CAFqBoqpuVYEZDZcgmAL8nSi1mHH8yOBH4EdJKV_asnmYqLFVGw@mail.gmail.com>

Hi,

I am trying to process nifti-1 images using HDFS and I was wondering if it
was possible to read an image's byte stream into nibabel as I want to avoid
saving the image locally.

Thanks,

Valerie
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From effigies at bu.edu  Wed Feb 22 14:51:43 2017
From: effigies at bu.edu (Christopher Markiewicz)
Date: Wed, 22 Feb 2017 14:51:43 -0500
Subject: [Neuroimaging] Reading a byte stream into nibabel
In-Reply-To: <CAFqBoqpuVYEZDZcgmAL8nSi1mHH8yOBH4EdJKV_asnmYqLFVGw@mail.gmail.com>
References: <CAFqBoqpuVYEZDZcgmAL8nSi1mHH8yOBH4EdJKV_asnmYqLFVGw@mail.gmail.com>
Message-ID: <CAHE-diPst2Sdfa+uYeJfksLRHOO2RhWdx1W=mC+weQ+tBU2arA@mail.gmail.com>

Hi Valerie,

Assuming that it's not gzipped, you can do something like:

    from io import BytesIO
    from nibabel import FileHolder, Nifti1Image
    fh = FileHolder(fileobj=BytesIO(input_stream))
    img = Nifti1Image.from_filemap({'header': fh, 'image': fh})

If it is gzipped, adjust accordingly:

    from gzip import GzipFile
    fh = FileHolder(fileobj=GzipFile(fileobj=BytesIO(input_stream)))

Cheers,
Chris


On Wed, Feb 22, 2017 at 2:22 PM, val hs <valeriehayot at gmail.com> wrote:

> Hi,
>
> I am trying to process nifti-1 images using HDFS and I was wondering if it
> was possible to read an image's byte stream into nibabel as I want to avoid
> saving the image locally.
>
> Thanks,
>
> Valerie
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From valeriehayot at gmail.com  Wed Feb 22 16:46:41 2017
From: valeriehayot at gmail.com (val hs)
Date: Wed, 22 Feb 2017 16:46:41 -0500
Subject: [Neuroimaging] Reading a byte stream into nibabel
In-Reply-To: <CAHE-diPst2Sdfa+uYeJfksLRHOO2RhWdx1W=mC+weQ+tBU2arA@mail.gmail.com>
References: <CAFqBoqpuVYEZDZcgmAL8nSi1mHH8yOBH4EdJKV_asnmYqLFVGw@mail.gmail.com>
 <CAHE-diPst2Sdfa+uYeJfksLRHOO2RhWdx1W=mC+weQ+tBU2arA@mail.gmail.com>
Message-ID: <CAFqBoqqt+q95g5wzyFJC_ycFK5xPP7-cYOwaZy=Fhqta0Uw17g@mail.gmail.com>

Works great! Thanks!

Valerie

On Wed, Feb 22, 2017 at 2:51 PM, Christopher Markiewicz <effigies at bu.edu>
wrote:

> Hi Valerie,
>
> Assuming that it's not gzipped, you can do something like:
>
>     from io import BytesIO
>     from nibabel import FileHolder, Nifti1Image
>     fh = FileHolder(fileobj=BytesIO(input_stream))
>     img = Nifti1Image.from_filemap({'header': fh, 'image': fh})
>
> If it is gzipped, adjust accordingly:
>
>     from gzip import GzipFile
>     fh = FileHolder(fileobj=GzipFile(fileobj=BytesIO(input_stream)))
>
> Cheers,
> Chris
>
>
> On Wed, Feb 22, 2017 at 2:22 PM, val hs <valeriehayot at gmail.com> wrote:
>
>> Hi,
>>
>> I am trying to process nifti-1 images using HDFS and I was wondering if
>> it was possible to read an image's byte stream into nibabel as I want to
>> avoid saving the image locally.
>>
>> Thanks,
>>
>> Valerie
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From jevillalonr at gmail.com  Wed Feb 22 17:14:41 2017
From: jevillalonr at gmail.com (Julio Villalon)
Date: Wed, 22 Feb 2017 14:14:41 -0800
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CA+X4w0xKj59QoWbA7AZhUHnkTZ_n_XJhPH-OM5r92pZYBgDYTg@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
 <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
 <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>
 <CACydq8oV+o4Q0TBV9jMK-8fk-e1ShCDQyiSFUArzD91zf+eFsg@mail.gmail.com>
 <CAKLc09+wF7dx2K-s-_U7yvzRvEa1VPgkzP01Wg81Vrhye61PbQ@mail.gmail.com>
 <CAN6JmWOh6N4dnXRdG_34ngx8u6DOjsG7vnTXxcNDbWecuRE5Ow@mail.gmail.com>
 <CA+X4w0xKj59QoWbA7AZhUHnkTZ_n_XJhPH-OM5r92pZYBgDYTg@mail.gmail.com>
Message-ID: <CAJ+byPSJEX2fEGjgGduhwVUUs98+0RMVstjtXTseqXHGWKNKGw@mail.gmail.com>

Hey everyone!  When are we meeting? on the 23rd or the 24th?

Cheers

Julio

2017-02-16 21:23 GMT-08:00 Ariel Rokem <arokem at gmail.com>:

>
> On Thu, Feb 16, 2017 at 9:52 AM, Eleftherios Garyfallidis <
> elef at indiana.edu> wrote:
>
>> Wait we can change the time. I didn't realize that it will be so early in
>> Europe. My bad! Let me share a doodle!
>> We may have the problem now that it maybe too early/late in Asia.
>>
>> Here is the link!
>>
>> http://doodle.com/poll/c2qiayevwczh9e24
>>
>>
> Sorry - I can't make any of these times. If you could please take notes,
> we can follow up here asynchronously after you have that discussion.
>
>
>> Best,
>> Eleftherios
>>
>>
>>
>> On Thu, Feb 16, 2017 at 12:42 PM Stephan Meesters <
>> stephan.meesters at gmail.com> wrote:
>>
>>> Hi Eleftherios
>>>
>>> Sorry but it's not at a very convenient time for me (5 am). I don't
>>> think my brain functions at this time of day =)
>>>
>>> In any case I will be able to meet up at the ISMRM this year, but not at
>>> OHBM unfortunately. Maybe MICCAI.
>>>
>>> Regards Stephan
>>>
>>> On Thu, 16 Feb 2017 at 18:10, K. Serge <skab12 at gmail.com> wrote:
>>>
>>> Sorry, I mixed the date. I'll be there
>>>
>>> Serge K.
>>>
>>> 2017-02-16 13:33 GMT+01:00 K. Serge <skab12 at gmail.com>:
>>>
>>> Unfortunatly, i can't.
>>>
>>> Serge
>>>
>>> ps: In general, wednesday is complicated for me.
>>>
>>>
>>>
>>> 2017-02-16 5:04 GMT+01:00 Ariel Rokem <arokem at gmail.com>:
>>>
>>>
>>>
>>> On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <
>>> elef at indiana.edu> wrote:
>>>
>>> Hi all,
>>>
>>> It has been some time from the last time we had a developers meeting.
>>> And I think we really need
>>> to improve our coordination across the different sites. Thanks all for
>>> helping with the transition.
>>>
>>> Also apologies for not being so much active in github. As expected,
>>> starting a lab and teaching can bring
>>> some delays.
>>>
>>> So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
>>> should be okay for all the main DIPY centers (Asia, Europe, America).
>>> If you cannot attend then I 'll be happy to create a doodle.
>>>
>>> Here are some ideas for the agenda:
>>>
>>> - Releasing 12. Tomorrow will send a list of final PRs for the release.
>>> - Web transition. We have new website let's start using it.
>>> - GSoC mentors for 2017. I have already started a wiki
>>> https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
>>> - OHBM, MICCAI and Brainhack participations.
>>> - Other urgent topics. Compilation issues etc.
>>>
>>> I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
>>> Stephen. Of course the rest can join too.
>>>
>>>
>>> I'll be there.
>>>
>>> Ariel
>>>
>>>
>>> So, we should try to have a similar meeting once a month. And scientific
>>> hangouts once every 2 months.
>>> Let me know if you think otherwise.
>>>
>>> Crack on! 0.12 on the way! :)
>>>
>>> Best regards,
>>> Eleftherios
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From elef at indiana.edu  Thu Feb 23 13:11:52 2017
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Thu, 23 Feb 2017 18:11:52 +0000
Subject: [Neuroimaging] [DIPY] Re-igniting our awesome developer meetings
In-Reply-To: <CAJ+byPSJEX2fEGjgGduhwVUUs98+0RMVstjtXTseqXHGWKNKGw@mail.gmail.com>
References: <CAN6JmWNUv6xkou_rZY78uB9rhbhe_eOOpVChzbZuZpJhpgWmoQ@mail.gmail.com>
 <CA+X4w0z=qgMSbzs2q+8wK6yaCZ+qj2BfhyHbUVCTWs1XJwmPGA@mail.gmail.com>
 <CACydq8rDOQt8SCDt8hTXTvYST8Ugkp=3-eKZ8ag85nJcqO9KfQ@mail.gmail.com>
 <CACydq8oV+o4Q0TBV9jMK-8fk-e1ShCDQyiSFUArzD91zf+eFsg@mail.gmail.com>
 <CAKLc09+wF7dx2K-s-_U7yvzRvEa1VPgkzP01Wg81Vrhye61PbQ@mail.gmail.com>
 <CAN6JmWOh6N4dnXRdG_34ngx8u6DOjsG7vnTXxcNDbWecuRE5Ow@mail.gmail.com>
 <CA+X4w0xKj59QoWbA7AZhUHnkTZ_n_XJhPH-OM5r92pZYBgDYTg@mail.gmail.com>
 <CAJ+byPSJEX2fEGjgGduhwVUUs98+0RMVstjtXTseqXHGWKNKGw@mail.gmail.com>
Message-ID: <CAN6JmWP8ErTMkaGG_yr1XwoXkPULRBt3OTHABWYVMPS=J+6++g@mail.gmail.com>

Okay given the current extreme schedule changes.
Will delay this meeting. And get back with better times for everyone!

Didn't realize tomorrow is Marc-Alex PhD defense! OMG! Best of luck!
I am sure you will rock!

More on this asap!
:)



On Wed, Feb 22, 2017 at 5:15 PM Julio Villalon <jevillalonr at gmail.com>
wrote:

> Hey everyone!  When are we meeting? on the 23rd or the 24th?
>
> Cheers
>
> Julio
>
> 2017-02-16 21:23 GMT-08:00 Ariel Rokem <arokem at gmail.com>:
>
>
> On Thu, Feb 16, 2017 at 9:52 AM, Eleftherios Garyfallidis <
> elef at indiana.edu> wrote:
>
> Wait we can change the time. I didn't realize that it will be so early in
> Europe. My bad! Let me share a doodle!
> We may have the problem now that it maybe too early/late in Asia.
>
> Here is the link!
>
> http://doodle.com/poll/c2qiayevwczh9e24
>
>
> Sorry - I can't make any of these times. If you could please take notes,
> we can follow up here asynchronously after you have that discussion.
>
>
> Best,
> Eleftherios
>
>
>
> On Thu, Feb 16, 2017 at 12:42 PM Stephan Meesters <
> stephan.meesters at gmail.com> wrote:
>
> Hi Eleftherios
>
> Sorry but it's not at a very convenient time for me (5 am). I don't think
> my brain functions at this time of day =)
>
> In any case I will be able to meet up at the ISMRM this year, but not at
> OHBM unfortunately. Maybe MICCAI.
>
> Regards Stephan
>
> On Thu, 16 Feb 2017 at 18:10, K. Serge <skab12 at gmail.com> wrote:
>
> Sorry, I mixed the date. I'll be there
>
> Serge K.
>
> 2017-02-16 13:33 GMT+01:00 K. Serge <skab12 at gmail.com>:
>
> Unfortunatly, i can't.
>
> Serge
>
> ps: In general, wednesday is complicated for me.
>
>
>
> 2017-02-16 5:04 GMT+01:00 Ariel Rokem <arokem at gmail.com>:
>
>
>
> On Wed, Feb 15, 2017 at 4:15 PM, Eleftherios Garyfallidis <
> elef at indiana.edu> wrote:
>
> Hi all,
>
> It has been some time from the last time we had a developers meeting. And
> I think we really need
> to improve our coordination across the different sites. Thanks all for
> helping with the transition.
>
> Also apologies for not being so much active in github. As expected,
> starting a lab and teaching can bring
> some delays.
>
> So, I suggest we meet next Thursday (Feb 23rd) at 11pm EST. This time
> should be okay for all the main DIPY centers (Asia, Europe, America).
> If you cannot attend then I 'll be happy to create a doodle.
>
> Here are some ideas for the agenda:
>
> - Releasing 12. Tomorrow will send a list of final PRs for the release.
> - Web transition. We have new website let's start using it.
> - GSoC mentors for 2017. I have already started a wiki
> https://github.com/nipy/dipy/wiki/Google-Summer-of-Code-2017
> - OHBM, MICCAI and Brainhack participations.
> - Other urgent topics. Compilation issues etc.
>
> I will like to see in this meeting Ariel, Serge, Rafael, JC, Julio, and
> Stephen. Of course the rest can join too.
>
>
> I'll be there.
>
> Ariel
>
>
> So, we should try to have a similar meeting once a month. And scientific
> hangouts once every 2 months.
> Let me know if you think otherwise.
>
> Crack on! 0.12 on the way! :)
>
> Best regards,
> Eleftherios
>
>
>
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From jevillalonr at gmail.com  Thu Feb 23 20:36:42 2017
From: jevillalonr at gmail.com (Julio Villalon)
Date: Thu, 23 Feb 2017 17:36:42 -0800
Subject: [Neuroimaging] [Nilearn] Problem with joblib when running the
 SpaceNet classifier
Message-ID: <CAJ+byPSb7kR4+v0r450SWkXU2zgKgcyhJ9XwhekRc2srEqfdYA@mail.gmail.com>

Hi Nilearn team,

I am trying to run the SpaceNet example:

https://nilearn.github.io/auto_examples/02_decoding/plot_haxby_space_net.html#sphx-glr-auto-examples-02-decoding-plot-haxby-space-net-py

And I am getting the following error:

' ' '
ValueError: Found array with 0 sample(s) (shape=(0, 129600)) while a
minimum of 1 is required.

/Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133:
DeprecationWarning: The file
'nilearn_cache/joblib/nilearn/masking/compute_epi_mask/8ac3f6747d8c3cbe01809029506bc2c4/output.pkl'
has been generated with a joblib version less than 0.10. Please regenerate
this pickle file.
  return numpy_pickle.load(filename, mmap_mode=mmap_mode)
' ' '

I am using Python 3.5, Numpy 1.12, Scipy 0.18.1. I also included in my
PYTHONPATH the latest development versions (master branches) of Nilearn and
Scikit-learn.

Can anyone point me in the right direction of how to solve this problem?

Thank you

Julio Villalon
USC Imaging Genetics Center

This is full error message:
------------------------------------------------
Traceback (most recent call last):
  File
"/Users/jvillalo/anaconda/lib/python3.5/site-packages/IPython/core/interactiveshell.py",
line 2481, in safe_execfile
    self.compile if kw['shell_futures'] else None)
  File
"/Users/jvillalo/anaconda/lib/python3.5/site-packages/IPython/utils/py3compat.py",
line 186, in execfile
    exec(compiler(f.read(), fname, 'exec'), glob, loc)
  File
"/Users/jvillalo/Documents/IGC/Conferences/MICCAI_2016/Gaels_code/plot_haxby_space_net.py",
line 70, in <module>
    decoder.fit(X_train, y_train)
  File "/Users/jvillalo/nilearn/nilearn/decoding/space_net.py", line 783,
in fit
    multi_output=True, y_numeric=True)
  File
"/Users/jvillalo/nilearn/nilearn/_utils/fixes/sklearn_validation.py", line
195, in check_X_y
    ensure_min_features)
  File
"/Users/jvillalo/nilearn/nilearn/_utils/fixes/sklearn_validation.py", line
97, in check_array
    % (n_samples, shape_repr, ensure_min_samples))
ValueError: Found array with 0 sample(s) (shape=(0, 129600)) while a
minimum of 1 is required.

/Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133:
DeprecationWarning: The file
'nilearn_cache/joblib/nilearn/masking/compute_epi_mask/8ac3f6747d8c3cbe01809029506bc2c4/output.pkl'
has been generated with a joblib version less than 0.10. Please regenerate
this pickle file.
  return numpy_pickle.load(filename, mmap_mode=mmap_mode)
/Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133:
DeprecationWarning: The file
'nilearn_cache/joblib/nilearn/image/resampling/resample_img/ea3a4d90803321dbf749b23ff6acfa18/output.pkl'
has been generated with a joblib version less than 0.10. Please regenerate
this pickle file.
  return numpy_pickle.load(filename, mmap_mode=mmap_mode)

-------------------------------------------------------------
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From gael.varoquaux at normalesup.org  Fri Feb 24 01:31:44 2017
From: gael.varoquaux at normalesup.org (Gael Varoquaux)
Date: Fri, 24 Feb 2017 07:31:44 +0100
Subject: [Neuroimaging] [Nilearn] Problem with joblib when running the
 SpaceNet classifier
In-Reply-To: <CAJ+byPSb7kR4+v0r450SWkXU2zgKgcyhJ9XwhekRc2srEqfdYA@mail.gmail.com>
References: <CAJ+byPSb7kR4+v0r450SWkXU2zgKgcyhJ9XwhekRc2srEqfdYA@mail.gmail.com>
Message-ID: <20170224063144.GB67401@phare.normalesup.org>

On Thu, Feb 23, 2017 at 05:36:42PM -0800, Julio Villalon wrote:
> /Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133:
> DeprecationWarning: The file 'nilearn_cache/joblib/nilearn/masking/
> compute_epi_mask/8ac3f6747d8c3cbe01809029506bc2c4/output.pkl' has been
> generated with a joblib version less than 0.10. Please regenerate this pickle
> file.
> ? return numpy_pickle.load(filename, mmap_mode=mmap_mode)
> ' ' '?

Try erasing the cache directory: nilearn_cache/joblib

G

From bertrand.thirion at inria.fr  Sat Feb 25 15:09:49 2017
From: bertrand.thirion at inria.fr (bthirion)
Date: Sat, 25 Feb 2017 21:09:49 +0100
Subject: [Neuroimaging] [Nilearn] Problem with joblib when running the
 SpaceNet classifier
In-Reply-To: <CAJ+byPSb7kR4+v0r450SWkXU2zgKgcyhJ9XwhekRc2srEqfdYA@mail.gmail.com>
References: <CAJ+byPSb7kR4+v0r450SWkXU2zgKgcyhJ9XwhekRc2srEqfdYA@mail.gmail.com>
Message-ID: <2484de59-2d79-40d9-ed22-dc7f1616b706@inria.fr>

     Dear Julio,

     Given the warnings on compute_epi_mask, I think that you should 
remove the folder nilearn_cache/joblib/nilearn/masking/compute_epi_mask 
and launch again.
     Best,

Bertrand Thirion


On 24/02/2017 02:36, Julio Villalon wrote:
> Hi Nilearn team,
>
> I am trying to run the SpaceNet example:
>
> https://nilearn.github.io/auto_examples/02_decoding/plot_haxby_space_net.html#sphx-glr-auto-examples-02-decoding-plot-haxby-space-net-py
>
> And I am getting the following error:
>
> ' ' '
> ValueError: Found array with 0 sample(s) (shape=(0, 129600)) while a 
> minimum of 1 is required.
>
> /Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133: 
> DeprecationWarning: The file 
> 'nilearn_cache/joblib/nilearn/masking/compute_epi_mask/8ac3f6747d8c3cbe01809029506bc2c4/output.pkl' 
> has been generated with a joblib version less than 0.10. Please 
> regenerate this pickle file.
>   return numpy_pickle.load(filename, mmap_mode=mmap_mode)
> ' ' '
>
> I am using Python 3.5, Numpy 1.12, Scipy 0.18.1. I also included in my 
> PYTHONPATH the latest development versions (master branches) of 
> Nilearn and Scikit-learn.
>
> Can anyone point me in the right direction of how to solve this problem?
>
> Thank you
>
> Julio Villalon
> USC Imaging Genetics Center
>
> This is full error message:
> ------------------------------------------------
> Traceback (most recent call last):
>   File 
> "/Users/jvillalo/anaconda/lib/python3.5/site-packages/IPython/core/interactiveshell.py", 
> line 2481, in safe_execfile
>     self.compile if kw['shell_futures'] else None)
>   File 
> "/Users/jvillalo/anaconda/lib/python3.5/site-packages/IPython/utils/py3compat.py", 
> line 186, in execfile
>     exec(compiler(f.read(), fname, 'exec'), glob, loc)
>   File 
> "/Users/jvillalo/Documents/IGC/Conferences/MICCAI_2016/Gaels_code/plot_haxby_space_net.py", 
> line 70, in <module>
>     decoder.fit(X_train, y_train)
>   File "/Users/jvillalo/nilearn/nilearn/decoding/space_net.py", line 
> 783, in fit
>     multi_output=True, y_numeric=True)
>   File 
> "/Users/jvillalo/nilearn/nilearn/_utils/fixes/sklearn_validation.py", 
> line 195, in check_X_y
>     ensure_min_features)
>   File 
> "/Users/jvillalo/nilearn/nilearn/_utils/fixes/sklearn_validation.py", 
> line 97, in check_array
>     % (n_samples, shape_repr, ensure_min_samples))
> ValueError: Found array with 0 sample(s) (shape=(0, 129600)) while a 
> minimum of 1 is required.
>
> /Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133: 
> DeprecationWarning: The file 
> 'nilearn_cache/joblib/nilearn/masking/compute_epi_mask/8ac3f6747d8c3cbe01809029506bc2c4/output.pkl' 
> has been generated with a joblib version less than 0.10. Please 
> regenerate this pickle file.
>   return numpy_pickle.load(filename, mmap_mode=mmap_mode)
> /Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133: 
> DeprecationWarning: The file 
> 'nilearn_cache/joblib/nilearn/image/resampling/resample_img/ea3a4d90803321dbf749b23ff6acfa18/output.pkl' 
> has been generated with a joblib version less than 0.10. Please 
> regenerate this pickle file.
>   return numpy_pickle.load(filename, mmap_mode=mmap_mode)
>
> -------------------------------------------------------------
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging


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From effigies at bu.edu  Mon Feb 27 17:38:23 2017
From: effigies at bu.edu (Christopher Markiewicz)
Date: Mon, 27 Feb 2017 17:38:23 -0500
Subject: [Neuroimaging] Announcing Quickshear v1.0
Message-ID: <CAHE-diOugOP9TS8fncD9LARCbtX63kbtPGSTaHrAFGFpz1yjHQ@mail.gmail.com>

Hi all,

Quickshear[0] is a defacing utility that calculates the convex-hull of a
skull-stripped brain to split the volume into brain and face regions, and
then zeros out the face region of an anatomical image. It comes out of a
computer security lab that had a brief flurry of activity in neuroimaging
privacy a few years back.

I contacted the authors a couple weeks ago to try it out, and they kindly
agreed to let me publish it. As it is a standalone program, rather than
immediately try to include it in existing projects, I've made some very
minor modifications and released their code as v1.0 to stand as a reference
implementation.

Beyond this reference implementation, though, I'm not committed to the idea
that it must be a separate project; while I'm happy to maintain it in this
form, if a larger existing project would like to include it, that would
only lower the barrier to use.

Best,
Chris Markiewicz

[0]
https://www.researchgate.net/publication/262319696_Quickshear_defacing_for_neuroimages
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From effigies at bu.edu  Tue Feb 28 10:21:24 2017
From: effigies at bu.edu (Christopher Markiewicz)
Date: Tue, 28 Feb 2017 10:21:24 -0500
Subject: [Neuroimaging] Announcing Quickshear v1.0
In-Reply-To: <CAHE-diOugOP9TS8fncD9LARCbtX63kbtPGSTaHrAFGFpz1yjHQ@mail.gmail.com>
References: <CAHE-diOugOP9TS8fncD9LARCbtX63kbtPGSTaHrAFGFpz1yjHQ@mail.gmail.com>
Message-ID: <CAHE-diN8exypGUmju_YujcySZk-kMoHsR9TWrQbwKHbuGFoO3w@mail.gmail.com>

Woops. Apparently didn't include a link.

Here's the Quickshear v1.0 release:
https://github.com/nipy/quickshear/releases/tag/v1.0

Best,
Chris Markiewicz

On Mon, Feb 27, 2017 at 5:38 PM, Christopher Markiewicz <effigies at bu.edu>
wrote:

> Hi all,
>
> Quickshear[0] is a defacing utility that calculates the convex-hull of a
> skull-stripped brain to split the volume into brain and face regions, and
> then zeros out the face region of an anatomical image. It comes out of a
> computer security lab that had a brief flurry of activity in neuroimaging
> privacy a few years back.
>
> I contacted the authors a couple weeks ago to try it out, and they kindly
> agreed to let me publish it. As it is a standalone program, rather than
> immediately try to include it in existing projects, I've made some very
> minor modifications and released their code as v1.0 to stand as a reference
> implementation.
>
> Beyond this reference implementation, though, I'm not committed to the
> idea that it must be a separate project; while I'm happy to maintain it in
> this form, if a larger existing project would like to include it, that
> would only lower the barrier to use.
>
> Best,
> Chris Markiewicz
>
> [0] https://www.researchgate.net/publication/262319696_
> Quickshear_defacing_for_neuroimages
>
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From matthew.brett at gmail.com  Tue Feb 28 13:05:50 2017
From: matthew.brett at gmail.com (Matthew Brett)
Date: Tue, 28 Feb 2017 10:05:50 -0800
Subject: [Neuroimaging] Announcing Quickshear v1.0
In-Reply-To: <CAHE-diN8exypGUmju_YujcySZk-kMoHsR9TWrQbwKHbuGFoO3w@mail.gmail.com>
References: <CAHE-diOugOP9TS8fncD9LARCbtX63kbtPGSTaHrAFGFpz1yjHQ@mail.gmail.com>
 <CAHE-diN8exypGUmju_YujcySZk-kMoHsR9TWrQbwKHbuGFoO3w@mail.gmail.com>
Message-ID: <CAH6Pt5pcH6P7MffnM6+pUKNASDoDO-bFFx7mZBDJuTiDjhsD9w@mail.gmail.com>

Hi Chris,

On Tue, Feb 28, 2017 at 7:21 AM, Christopher Markiewicz <effigies at bu.edu> wrote:
> Woops. Apparently didn't include a link.
>
> Here's the Quickshear v1.0 release:
> https://github.com/nipy/quickshear/releases/tag/v1.0
>
> Best,
> Chris Markiewicz
>
> On Mon, Feb 27, 2017 at 5:38 PM, Christopher Markiewicz <effigies at bu.edu>
> wrote:
>>
>> Hi all,
>>
>> Quickshear[0] is a defacing utility that calculates the convex-hull of a
>> skull-stripped brain to split the volume into brain and face regions, and
>> then zeros out the face region of an anatomical image. It comes out of a
>> computer security lab that had a brief flurry of activity in neuroimaging
>> privacy a few years back.
>>
>> I contacted the authors a couple weeks ago to try it out, and they kindly
>> agreed to let me publish it. As it is a standalone program, rather than
>> immediately try to include it in existing projects, I've made some very
>> minor modifications and released their code as v1.0 to stand as a reference
>> implementation.
>>
>> Beyond this reference implementation, though, I'm not committed to the
>> idea that it must be a separate project; while I'm happy to maintain it in
>> this form, if a larger existing project would like to include it, that would
>> only lower the barrier to use.

Thanks a lot for doing this - it looks very useful.

Cheers,

Matthew

From jevillalonr at gmail.com  Tue Feb 28 16:50:30 2017
From: jevillalonr at gmail.com (Julio Villalon)
Date: Tue, 28 Feb 2017 13:50:30 -0800
Subject: [Neuroimaging] [Nilearn] Problem with joblib when running the
 SpaceNet classifier
In-Reply-To: <2484de59-2d79-40d9-ed22-dc7f1616b706@inria.fr>
References: <CAJ+byPSb7kR4+v0r450SWkXU2zgKgcyhJ9XwhekRc2srEqfdYA@mail.gmail.com>
 <2484de59-2d79-40d9-ed22-dc7f1616b706@inria.fr>
Message-ID: <CAJ+byPTvoH9EEOngezkuGZdskY6WMovmfD65ecaH8WK7_matiw@mail.gmail.com>

Thanks a lot!  It worked!



2017-02-25 12:09 GMT-08:00 bthirion <bertrand.thirion at inria.fr>:

>     Dear Julio,
>
>     Given the warnings on compute_epi_mask, I think that you should remove
> the folder nilearn_cache/joblib/nilearn/masking/compute_epi_mask and
> launch again.
>     Best,
>
> Bertrand Thirion
>
>
>
> On 24/02/2017 02:36, Julio Villalon wrote:
>
> Hi Nilearn team,
>
> I am trying to run the SpaceNet example:
>
> https://nilearn.github.io/auto_examples/02_decoding/
> plot_haxby_space_net.html#sphx-glr-auto-examples-02-
> decoding-plot-haxby-space-net-py
>
> And I am getting the following error:
>
> ' ' '
> ValueError: Found array with 0 sample(s) (shape=(0, 129600)) while a
> minimum of 1 is required.
>
> /Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133:
> DeprecationWarning: The file 'nilearn_cache/joblib/nilearn/
> masking/compute_epi_mask/8ac3f6747d8c3cbe01809029506bc2c4/output.pkl' has
> been generated with a joblib version less than 0.10. Please regenerate this
> pickle file.
>   return numpy_pickle.load(filename, mmap_mode=mmap_mode)
> ' ' '
>
> I am using Python 3.5, Numpy 1.12, Scipy 0.18.1. I also included in my
> PYTHONPATH the latest development versions (master branches) of Nilearn and
> Scikit-learn.
>
> Can anyone point me in the right direction of how to solve this problem?
>
> Thank you
>
> Julio Villalon
> USC Imaging Genetics Center
>
> This is full error message:
> ------------------------------------------------
> Traceback (most recent call last):
>   File "/Users/jvillalo/anaconda/lib/python3.5/site-packages/
> IPython/core/interactiveshell.py", line 2481, in safe_execfile
>     self.compile if kw['shell_futures'] else None)
>   File "/Users/jvillalo/anaconda/lib/python3.5/site-packages/IPython/utils/py3compat.py",
> line 186, in execfile
>     exec(compiler(f.read(), fname, 'exec'), glob, loc)
>   File "/Users/jvillalo/Documents/IGC/Conferences/MICCAI_2016/
> Gaels_code/plot_haxby_space_net.py", line 70, in <module>
>     decoder.fit(X_train, y_train)
>   File "/Users/jvillalo/nilearn/nilearn/decoding/space_net.py", line 783,
> in fit
>     multi_output=True, y_numeric=True)
>   File "/Users/jvillalo/nilearn/nilearn/_utils/fixes/sklearn_validation.py",
> line 195, in check_X_y
>     ensure_min_features)
>   File "/Users/jvillalo/nilearn/nilearn/_utils/fixes/sklearn_validation.py",
> line 97, in check_array
>     % (n_samples, shape_repr, ensure_min_samples))
> ValueError: Found array with 0 sample(s) (shape=(0, 129600)) while a
> minimum of 1 is required.
>
> /Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133:
> DeprecationWarning: The file 'nilearn_cache/joblib/nilearn/
> masking/compute_epi_mask/8ac3f6747d8c3cbe01809029506bc2c4/output.pkl' has
> been generated with a joblib version less than 0.10. Please regenerate this
> pickle file.
>   return numpy_pickle.load(filename, mmap_mode=mmap_mode)
> /Users/jvillalo/scikit-learn/sklearn/externals/joblib/memory.py:133:
> DeprecationWarning: The file 'nilearn_cache/joblib/nilearn/
> image/resampling/resample_img/ea3a4d90803321dbf749b23ff6acfa18/output.pkl'
> has been generated with a joblib version less than 0.10. Please regenerate
> this pickle file.
>   return numpy_pickle.load(filename, mmap_mode=mmap_mode)
>
> -------------------------------------------------------------
>
>
> _______________________________________________
> Neuroimaging mailing listNeuroimaging at python.orghttps://mail.python.org/mailman/listinfo/neuroimaging
>
>
>
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