From markiewicz at stanford.edu  Fri Mar  1 11:18:42 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Fri, 1 Mar 2019 16:18:42 +0000
Subject: [Neuroimaging] [nibabel] Future directions
Message-ID: <BN6PR02MB2675C396D258D5E33A24D3CCA9760@BN6PR02MB2675.namprd02.prod.outlook.com>

Hi all,

Just want to advertise a little more widely that I'm seeking input on the future of nibabel over on the GitHub issues page. In particular, I want to establish a predictable release schedule [0] and a timeline for deprecating Python 2 support [1]. I'm happy to extend this to any concerns or desires that you may have, but I think these two issues have the potential to be more disruptive than our usual process, so want to get feedback sooner than later.

[0] https://github.com/nipy/nibabel/issues/734
[1] https://github.com/nipy/nibabel/issues/735

--?
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University

From lewis.dunne00 at gmail.com  Sat Mar  2 04:37:50 2019
From: lewis.dunne00 at gmail.com (Lewis Dunne)
Date: Sat, 2 Mar 2019 09:37:50 +0000
Subject: [Neuroimaging] ROI BOLD extraction
Message-ID: <5c7a4ef0.1c69fb81.42b1e.14b7@mx.google.com>

Hello! I?m new to this list and have not yet started using NiPy, but have had a look through the docs and have a question.

I have a bunch of preprocessed fMRI .nii files that I?ve been using in MATLAB. With NiPy, is it possible to define a spherical region of interest, of any given radius, and extract the BOLD signal from this ROI across all .nii files in a directory for further analysis? IF so could somebody please point me in the right direction for how to achieve this?

Thanks in advance

Sent from Mail for Windows 10



---
This email has been checked for viruses by Avast antivirus software.
https://www.avast.com/antivirus
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From christophe at pallier.org  Sat Mar  2 04:47:34 2019
From: christophe at pallier.org (Christophe Pallier)
Date: Sat, 2 Mar 2019 10:47:34 +0100
Subject: [Neuroimaging] ROI BOLD extraction
In-Reply-To: <5c7a4ef0.1c69fb81.42b1e.14b7@mx.google.com>
References: <5c7a4ef0.1c69fb81.42b1e.14b7@mx.google.com>
Message-ID: <CALyk9bw_Z_Uo5WtaToOt+7u6ktdKMC07YG0fb=qD5mFMJ2L78Q@mail.gmail.com>

A function that does that  is available here (in nilearn):

https://nilearn.github.io/modules/generated/nilearn.input_data.NiftiSpheresMasker.html

See https://github.com/nilearn/nilearn/issues/1192



On Sat, Mar 2, 2019 at 10:38 AM Lewis Dunne <lewis.dunne00 at gmail.com> wrote:

> Hello! I?m new to this list and have not yet started using NiPy, but have
> had a look through the docs and have a question.
>
>
>
> I have a bunch of preprocessed fMRI .nii files that I?ve been using in
> MATLAB. With NiPy, is it possible to define a spherical region of interest,
> of any given radius, and extract the BOLD signal from this ROI across all
> .nii files in a directory for further analysis? IF so could somebody please
> point me in the right direction for how to achieve this?
>
>
>
> Thanks in advance
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
>
> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> Virus-free.
> www.avast.com
> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
> <#m_6923512596326005393_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>


-- 
--
Christophe Pallier <christophe at pallier.org>
INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,
91191 Gif-sur-Yvette Cedex, France
Tel: 00 33 1 69 08 79 34
Personal web site: http://www.pallier.org
Lab web site: http://www.unicog.org
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From christophe at pallier.org  Sat Mar  2 04:49:29 2019
From: christophe at pallier.org (Christophe Pallier)
Date: Sat, 2 Mar 2019 10:49:29 +0100
Subject: [Neuroimaging] ROI BOLD extraction
In-Reply-To: <CALyk9bw_Z_Uo5WtaToOt+7u6ktdKMC07YG0fb=qD5mFMJ2L78Q@mail.gmail.com>
References: <5c7a4ef0.1c69fb81.42b1e.14b7@mx.google.com>
 <CALyk9bw_Z_Uo5WtaToOt+7u6ktdKMC07YG0fb=qD5mFMJ2L78Q@mail.gmail.com>
Message-ID: <CALyk9bx1Z2oK=Xzm4U8obd+0yTDALRwBfB+1TkpDUZu1-VQhHw@mail.gmail.com>

Better example at
http://nilearn.github.io/auto_examples/03_connectivity/plot_seed_to_voxel_correlation.html

On Sat, Mar 2, 2019 at 10:47 AM Christophe Pallier <christophe at pallier.org>
wrote:

> A function that does that  is available here (in nilearn):
>
>
> https://nilearn.github.io/modules/generated/nilearn.input_data.NiftiSpheresMasker.html
>
> See https://github.com/nilearn/nilearn/issues/1192
>
>
>
> On Sat, Mar 2, 2019 at 10:38 AM Lewis Dunne <lewis.dunne00 at gmail.com>
> wrote:
>
>> Hello! I?m new to this list and have not yet started using NiPy, but have
>> had a look through the docs and have a question.
>>
>>
>>
>> I have a bunch of preprocessed fMRI .nii files that I?ve been using in
>> MATLAB. With NiPy, is it possible to define a spherical region of interest,
>> of any given radius, and extract the BOLD signal from this ROI across all
>> .nii files in a directory for further analysis? IF so could somebody please
>> point me in the right direction for how to achieve this?
>>
>>
>>
>> Thanks in advance
>>
>>
>>
>> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
>> Windows 10
>>
>>
>>
>>
>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> Virus-free.
>> www.avast.com
>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
>> <#m_-8423920077764006380_m_6923512596326005393_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
>
> --
> --
> Christophe Pallier <christophe at pallier.org>
> INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,
> 91191 Gif-sur-Yvette Cedex, France
> Tel: 00 33 1 69 08 79 34
> Personal web site: http://www.pallier.org
> Lab web site: http://www.unicog.org
>


-- 
--
Christophe Pallier <christophe at pallier.org>
INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,
91191 Gif-sur-Yvette Cedex, France
Tel: 00 33 1 69 08 79 34
Personal web site: http://www.pallier.org
Lab web site: http://www.unicog.org
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From matthieuvanhoutte at gmail.com  Sat Mar  2 10:34:06 2019
From: matthieuvanhoutte at gmail.com (Matthieu Vanhoutte)
Date: Sat, 2 Mar 2019 16:34:06 +0100
Subject: [Neuroimaging] PySurfer: RuntimeError: No pyface.toolkits plugin
 could be loaded for qt4
Message-ID: <283D5F73-CAE6-4B8B-8D03-A0F377B17F99@gmail.com>

Dear experts,

I tried to install PySurfer according guidelines on an OS X. However, when trying to launch a simple test with plot_basics.py, I got the following error message:

Traceback (most recent call last):
  File "plot_basics.py", line 8, in <module>
    from surfer import Brain
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/surfer/__init__.py", line 1, in <module>
    from .viz import Brain, TimeViewer  # noqa
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/surfer/viz.py", line 13, in <module>
    from mayavi import mlab
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/mayavi/mlab.py", line 15, in <module>
    from mayavi.core.common import process_ui_events
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/mayavi/core/common.py", line 21, in <module>
    from pyface import api as pyface
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/pyface/api.py", line 17, in <module>
    from .about_dialog import AboutDialog
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/pyface/about_dialog.py", line 19, in <module>
    from .toolkit import toolkit_object
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/pyface/toolkit.py", line 27, in <module>
    toolkit = toolkit_object = find_toolkit('pyface.toolkits')
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/pyface/base_toolkit.py", line 263, in find_toolkit
    return import_toolkit(ETSConfig.toolkit, entry_point)
  File "/Users/mattvan83/anaconda/envs/PySurf/lib/python3.7/site-packages/pyface/base_toolkit.py", line 227, in import_toolkit
    raise RuntimeError(msg)
RuntimeError: No pyface.toolkits plugin could be loaded for qt4

Could you help me about this error, I couldn?t find anything resolved on the web?

Best,
Matthieu
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From norkline at iu.edu  Sat Mar  2 17:28:11 2019
From: norkline at iu.edu (Kline, Nora Irene)
Date: Sat, 2 Mar 2019 22:28:11 +0000
Subject: [Neuroimaging] [Final Call - DIPY Workshop] Learn diffusion MRI
 Analysis in Python: March 11-15, 2019
Message-ID: <c5d94cc14efa41ca8d4d8b5bddfa9eb0@BL-CCI-D1S06.ads.iu.edu>


The DIPY Workshop is just 1 week away and we are super excited to see you there!?

Here is a short overview video from our founder:

VIDEO LINK: https://www.youtube.com/watch?v=NUb8pJg72w8



The DIPY<http://dipy.org/> (Diffusion Imaging in Python) workshop is a neuroimaging (Diffusion and Structural MRI Imaging) training and hacking event that the DIPY Team<https://workshop.dipy.org/#Speakers> is hosting at Indiana University, Bloomington, USA from March 11-15, 2019.

[cid:1dc19b97-a06c-438a-8edb-9e9981fcaf27]<http://?https:/workshop.dipy.org/>

The event is sponsored by the National Institute of Health (NIH)/ NIBIB. See speakers, topics and detailed information here:



https://workshop.dipy.org<https://workshop.dipy.org/>

The workshop will provide a series of tutorials including topics such as tractography, microstructure, and statistical analysis. All tutorials will be presented by esteemed instructors from a range of institutions and backgrounds. The workshop will also include a data accelerator where you will be able to analyze your own data together with the help of the instructors and DIPY<http://dipy.org/> developers.

This workshop will drastically help you advance your neuroimaging expertise and help you build analysis workflows that you can use for your research or other projects.

The workshop is intended at helping all kinds of researchers, clinical practitioners and industrial methods developers to get them more involved and well versed with using Python for neuroimaging research. The workshop will include social events, collaborative activities and hands-on development expertise.


Reserve your place for the DIPY Workshop 2019 - Titanium Edition today!


REGISTER HERE<https://workshop.dipy.org/#Home>


Please email us back at dipy at python.org<mailto:dipy at python.org> with any questions that you may have regarding schedule<https://workshop.dipy.org/#Schedule>, costs<https://workshop.dipy.org/#Registration>, accommodation<https://workshop.dipy.org/#Lodging>, etc. and we will be more than happy to help you out!



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From absalhalabi at gmail.com  Fri Mar  8 15:24:15 2019
From: absalhalabi at gmail.com (Abdullah Alhalabi)
Date: Fri, 8 Mar 2019 22:24:15 +0200
Subject: [Neuroimaging] Question about maximum intensity of nifti images
Message-ID: <CAFkODCWHg=YCLTwAXS6gMEE3Fd_wY_KCohpGrhYEebjyf01-Qw@mail.gmail.com>

Dear sirs

This is Abdullah Alhalabi, a biomedical engineering student at Jordan
university of science and technology, My graduation project is brain tumor
segmentation using deep neural network , I have downloaded the dataset that
I'm going to use, the images format is nifti , my problem that I want to
know the maximum display intensity of all the images and use it in scaling,
but when I display the image header it gives a 'cal_max' value of
zero(please find attached screen shot of the code), I searched a lot and I
didn't find any solution, I'll be very grateful if you help me.

Best regards
Abdullah Alhalabi
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From matthew.brett at gmail.com  Fri Mar  8 17:10:53 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 8 Mar 2019 22:10:53 +0000
Subject: [Neuroimaging] Question about maximum intensity of nifti images
In-Reply-To: <CAFkODCWHg=YCLTwAXS6gMEE3Fd_wY_KCohpGrhYEebjyf01-Qw@mail.gmail.com>
References: <CAFkODCWHg=YCLTwAXS6gMEE3Fd_wY_KCohpGrhYEebjyf01-Qw@mail.gmail.com>
Message-ID: <CAH6Pt5qVttFNysEq1KCOyKoOhWNw-dhJFZ-e9=9pHpiQi+Bk3g@mail.gmail.com>

Hi,

On Fri, Mar 8, 2019 at 10:08 PM Abdullah Alhalabi <absalhalabi at gmail.com> wrote:
>
> Dear sirs
>
> This is Abdullah Alhalabi, a biomedical engineering student at Jordan university of science and technology, My graduation project is brain tumor segmentation using deep neural network , I have downloaded the dataset that I'm going to use, the images format is nifti , my problem that I want to know the maximum display intensity of all the images and use it in scaling, but when I display the image header it gives a 'cal_max' value of zero(please find attached screen shot of the code), I searched a lot and I didn't find any solution, I'll be very grateful if you help me.
>

A lot of software doesn't write the cal_max field.   I think you'll
have to read in the values and get the maximum directly:

>>> np.max(img.get_fdata())

Cheers,

Matthew

From robbenson18 at gmail.com  Thu Mar 21 14:03:47 2019
From: robbenson18 at gmail.com (Roberto Guidotti)
Date: Thu, 21 Mar 2019 19:03:47 +0100
Subject: [Neuroimaging] [nilearn] Save partial searchlight results
Message-ID: <CAGj93cHHSeg-7O1q5MNcQ3fRGOftuDVpZitaGrMy8JTTtmWm8A@mail.gmail.com>

Hi everybody,

I am running a searchlight analysis using a Leave One Subject Out
Cross-Validation, the problem is that it needs a lot of time to perform the
analysis and I don't want to lose my results if something occurs like power
supply cut off or other issues.

I'd like to extend the searchlight functionalities in order to save partial
results somewhere, for example by using memmap.

Can you suggest an elegant approach to add this feature?

Thank you
Roberto
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From switt4 at uwo.ca  Thu Mar 28 16:08:28 2019
From: switt4 at uwo.ca (Suzanne Witt)
Date: Thu, 28 Mar 2019 20:08:28 +0000
Subject: [Neuroimaging] nibabel save returning NotImplementedError at
 _to_xml_element
Message-ID: <3D6C9536-E222-49CD-8FDC-0A1079493289@uwo.ca>

Hi,

I apologize if this has already been addressed in a previous message, but I did not find anything searching the archives from the Nibabel website.

I am running python 3.7.0 on a conda installation and recently installed the nibabel package to make use of its gifti class.

I have a python script that builds a gifti image object and fills in all of the meta data, label table, and data array details.  The script is based off of a matlab one that successfully makes use of Guillaume Flandin?s @gifti toolkit.  (Not sure if this is relevant or not, but the gifti image objects contains 30 separate data arrays, one for each of 30 individual subjects.)  I have compared my gifti image object?s structure and details to a similar one I loaded in to python using nibabel, and everything looks similar between the two.

When I go to save my newly created gifti image object out using nibabel.save, I am getting a ?NotImplementedError? in relation to _to_xml_element().  I am quite new to python, so I have no idea what the error means (a google search and digging through Stack Overflow didn?t yield much I could make sense of).  Trying to debug opened up xmlutils.py, where the only thing that seemed to be defined for _to_xml_element() was raising this NotImplementedError()...

Any suggestions as to how best to proceed?

I?m really not sure if this error is being thrown by something on my end or something on nibabel?s end, so I am happy to provide more details on my python script if that would help.

Thanks in advance,

suzanne



[cid:67412C66-BB70-409C-BE50-7BADCECDE5F9 at uwo-x-11.wireless.uwo.pri]

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From markiewicz at stanford.edu  Sun Mar 31 10:46:55 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Sun, 31 Mar 2019 14:46:55 +0000
Subject: [Neuroimaging] nibabel save returning NotImplementedError at
 _to_xml_element
In-Reply-To: <3D6C9536-E222-49CD-8FDC-0A1079493289@uwo.ca>
References: <3D6C9536-E222-49CD-8FDC-0A1079493289@uwo.ca>
Message-ID: <BN6PR02MB267535EF60577FE02E432BACA9540@BN6PR02MB2675.namprd02.prod.outlook.com>

Hi Suzanne,

>From what you say, it's hard to tell exactly what's going on. Are you able to share the code that you used to generate the error? Ideally something that can be copied and pasted into a python prompt, so if you have some real data you don't want to share, you can use numpy to generate random arrays:

import numpy as np
my_array = np.random.random((nrows, ncols))

Best,
Chris
________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Suzanne Witt <switt4 at uwo.ca>
Sent: Thursday, March 28, 2019 4:08 PM
To: neuroimaging at python.org
Subject: [Neuroimaging] nibabel save returning NotImplementedError at _to_xml_element

Hi,

I apologize if this has already been addressed in a previous message, but I did not find anything searching the archives from the Nibabel website.

I am running python 3.7.0 on a conda installation and recently installed the nibabel package to make use of its gifti class.

I have a python script that builds a gifti image object and fills in all of the meta data, label table, and data array details.  The script is based off of a matlab one that successfully makes use of Guillaume Flandin?s @gifti toolkit.  (Not sure if this is relevant or not, but the gifti image objects contains 30 separate data arrays, one for each of 30 individual subjects.)  I have compared my gifti image object?s structure and details to a similar one I loaded in to python using nibabel, and everything looks similar between the two.

When I go to save my newly created gifti image object out using nibabel.save, I am getting a ?NotImplementedError? in relation to _to_xml_element().  I am quite new to python, so I have no idea what the error means (a google search and digging through Stack Overflow didn?t yield much I could make sense of).  Trying to debug opened up xmlutils.py, where the only thing that seemed to be defined for _to_xml_element() was raising this NotImplementedError()...

Any suggestions as to how best to proceed?

I?m really not sure if this error is being thrown by something on my end or something on nibabel?s end, so I am happy to provide more details on my python script if that would help.

Thanks in advance,

suzanne



[cid:67412C66-BB70-409C-BE50-7BADCECDE5F9 at uwo-x-11.wireless.uwo.pri]

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