From Kiho.Im at childrens.harvard.edu Wed Jan 5 11:41:52 2022
From: Kiho.Im at childrens.harvard.edu (Im, Kiho)
Date: Wed, 5 Jan 2022 16:41:52 +0000
Subject: [Neuroimaging] Postdoctoral position in developmental neuroimaging
research at Harvard Medical School
Message-ID: <8BDF4DCB-DC92-4E7D-AC14-6175B5E74264@childrens.harvard.edu>
Postdoctoral position in developmental neuroimaging research at Harvard Medical School
A postdoctoral research fellow position is available in Dr. Im?s research lab (https://projects.iq.harvard.edu/neuroim) in the Fetal-Neonatal Neuroimaging & Developmental Science Center at Harvard Medical School and Boston Children?s Hospital. Dr. Im?s project has focused on developing and analyzing quantitative neuroimaging (structural, diffusion, and functional MRI) features in human fetuses and patients with genetic brain malformations and psychiatric/neurological brain disorders.
A postdoctoral researcher will develop a novel fetal structural/diffusion/functional MRI processing or analytic method using advanced mathematical, statistical, or deep learning techniques; investigate fetal/neonatal brain development (e.g., cortical plate and subplate thickness and cortical surface growth, brain development prediction) using surface-based and deep learning-based methods.
The Im lab is in the Fetal- Neonatal Neuroimaging and Developmental Science Center (https://www.fnndsc.org) where world-renowned professional researchers study brain development using various neuroimaging techniques such as MRI, Magnetoencephalography (MEG), and Near-Infrared Spectroscopy (NIRS) in fetuses, neonates, infants, and patients with developmental brain disorders. Thus, the postdoctoral researcher will also have great opportunities for various collaborations.
The candidates should have
- Ph.D degree in engineering or computer science
- Proficiency in programming, such as C++, Python, and Matlab
- Expertise in structural MRI processing and analysis (Experience of diffusion/functional MRI analysis is a plus) or machine learning/deep learning
To apply for this position, please send you CV, the list of 2~3 references with contact information, and a cover letter describing your research interests, most notable publications, and career goals to Kiho Im,
Kiho.Im at childrens.harvard.edu
Best,
Kiho
------------------------------------------------------------------------------------
Kiho Im, PhD
Assistant Professor of Pediatrics, Harvard Medical School
Fetal-Neonatal Neuroimaging & Developmental Science Center,
Division of Newborn Medicine, Boston Children's Hospital
Boston Children's Hospital
401 Park Dr., Boston, MA 02215
Kiho.Im at childrens.harvard.edu kiho.sky at gmail.com
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From bertrand.thirion at inria.fr Thu Jan 13 16:28:51 2022
From: bertrand.thirion at inria.fr (bthirion)
Date: Thu, 13 Jan 2022 22:28:51 +0100
Subject: [Neuroimaging] Developer for Nilearn
Message-ID:
?? ? Hi,
??? We?re hiring a developer for the support of Nilearn (Nilearn:
Statistical Analysis for NeuroImaging in Python ? Machine learning for
NeuroImaging). The position
will be with Parietal(Parietal ? Learning brain structure, function and
variability from neuroimaging data),
and in close collaboration with the EBRAINS
(https://ebrains.eu) European platform.
More info here:
https://team.inria.fr/parietal/files/2021/12/nistar.pdf
Applications are expected till the end of January 2022 .
Please forward !
Best,
Bertrand
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From eric.condamine at univ-grenoble-alpes.fr Fri Jan 14 10:27:08 2022
From: eric.condamine at univ-grenoble-alpes.fr (Eric Condamine)
Date: Fri, 14 Jan 2022 16:27:08 +0100 (CET)
Subject: [Neuroimaging] The process cannot access the file because it is
being used by another process ...
Message-ID: <1400398499.3453536.1642174028895.JavaMail.zimbra@univ-grenoble-alpes.fr>
Dear all,
I observe a small issue with nibabel only under Windows which unlike macos or linux does not allow to delete a file used by a process.
Minimum procedure to reproduce:
PS C:\Users\econd> python
Python 3.9.7 (tags/v3.9.7:1016ef3, Aug 30 2021, 20:19:38) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel as nib
>>> import os, sys
>>> b=nib.as_closest_canonical(nib.load('C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion- [ callto:2016-03-17083444-00 | 2016-03-17083444-00 ] -T13DSENSE-T1TFE-000425_000.nii'))
>>> b>>> os.remove('C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion- [ callto:2016-03-17083444-00 | 2016-03-17083444-00 ] -T13DSENSE-T1TFE-000425_000.nii')
Traceback (most recent call last): File "", line 1, in PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion- [ callto:2016-03-17083444-00 | 2016-03-17083444-00 ] -T13DSENSE-T1TFE-000425_000.nii'
Without going into details in order to not make you waste time unnecessarily, we need in some codes to have access to the b object (vide supra) and then in some cases to delete the file used in the instanciation of b. Under macos and linux no problem but under windows we have the PermissionError exception. How can we manage to delete the file? (del b is not enough!).
All the best for 2022!
Eric
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From markiewicz at stanford.edu Fri Jan 14 11:10:18 2022
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Fri, 14 Jan 2022 16:10:18 +0000
Subject: [Neuroimaging] The process cannot access the file because it is
being used by another process ...
In-Reply-To: <1400398499.3453536.1642174028895.JavaMail.zimbra@univ-grenoble-alpes.fr>
References: <1400398499.3453536.1642174028895.JavaMail.zimbra@univ-grenoble-alpes.fr>
Message-ID:
Hi Eric,
You may want to use `mmap=False` when loading to ensure that the data array is loaded into RAM rather than memory mapped. Apart from that, the file handles shouldn't be left open.
Best,
Chris
________________________________________
From: Neuroimaging on behalf of Eric Condamine
Sent: Friday, January 14, 2022 10:27
To: neuroimaging at python.org
Subject: [Neuroimaging] The process cannot access the file because it is being used by another process ...
Dear all,
I observe a small issue with nibabel only under Windows which unlike macos or linux does not allow to delete a file used by a process.
Minimum procedure to reproduce:
PS C:\Users\econd> python
Python 3.9.7 (tags/v3.9.7:1016ef3, Aug 30 2021, 20:19:38) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel as nib
>>> import os, sys
>>> b=nib.as_closest_canonical(nib.load('C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion-2016-03-17083444-00-T13DSENSE-T1TFE-000425_000.nii'))
>>> b>>> os.remove('C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion-2016-03-17083444-00-T13DSENSE-T1TFE-000425_000.nii')
Traceback (most recent call last): File "", line 1, in PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion-2016-03-17083444-00-T13DSENSE-T1TFE-000425_000.nii'
Without going into details in order to not make you waste time unnecessarily, we need in some codes to have access to the b object (vide supra) and then in some cases to delete the file used in the instanciation of b. Under macos and linux no problem but under windows we have the PermissionError exception. How can we manage to delete the file? (del b is not enough!).
All the best for 2022!
Eric
From eric.condamine at univ-grenoble-alpes.fr Mon Jan 17 06:19:39 2022
From: eric.condamine at univ-grenoble-alpes.fr (Eric Condamine)
Date: Mon, 17 Jan 2022 12:19:39 +0100 (CET)
Subject: [Neuroimaging] Neuroimaging Digest, Vol 80, Issue 3
In-Reply-To:
References:
Message-ID: <170983711.4688524.1642418379770.JavaMail.zimbra@univ-grenoble-alpes.fr>
Dear Chris,
This is exactly what I needed (and it gave me the idea to go a little further in reading the signatures in the nibabel documentation ;-))
Thanks a lot.
All the best.
Eric
De: neuroimaging-request at python.org
?: "neuroimaging"
Envoy?: Samedi 15 Janvier 2022 18:00:02
Objet: Neuroimaging Digest, Vol 80, Issue 3
Send Neuroimaging mailing list submissions to
neuroimaging at python.org
To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Neuroimaging digest..."
Today's Topics:
1. Re: The process cannot access the file because it is being
used by another process ... (Christopher Markiewicz)
----------------------------------------------------------------------
Message: 1
Date: Fri, 14 Jan 2022 16:10:18 +0000
From: Christopher Markiewicz
To: Neuroimaging analysis in Python
Subject: Re: [Neuroimaging] The process cannot access the file because
it is being used by another process ...
Message-ID:
Content-Type: text/plain; charset="us-ascii"
Hi Eric,
You may want to use `mmap=False` when loading to ensure that the data array is loaded into RAM rather than memory mapped. Apart from that, the file handles shouldn't be left open.
Best,
Chris
________________________________________
From: Neuroimaging on behalf of Eric Condamine
Sent: Friday, January 14, 2022 10:27
To: neuroimaging at python.org
Subject: [Neuroimaging] The process cannot access the file because it is being used by another process ...
Dear all,
I observe a small issue with nibabel only under Windows which unlike macos or linux does not allow to delete a file used by a process.
Minimum procedure to reproduce:
PS C:\Users\econd> python
Python 3.9.7 (tags/v3.9.7:1016ef3, Aug 30 2021, 20:19:38) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel as nib
>>> import os, sys
>>> b=nib.as_closest_canonical(nib.load('C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion-2016-03-17083444-00-T13DSENSE-T1TFE-000425_000.nii'))
>>> b>>> os.remove('C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion-2016-03-17083444-00-T13DSENSE-T1TFE-000425_000.nii')
Traceback (most recent call last): File "", line 1, in PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\econd\\Desktop\\test\\alej170316-IRMFonct_+perfusion-2016-03-17083444-00-T13DSENSE-T1TFE-000425_000.nii'
Without going into details in order to not make you waste time unnecessarily, we need in some codes to have access to the b object (vide supra) and then in some cases to delete the file used in the instanciation of b. Under macos and linux no problem but under windows we have the PermissionError exception. How can we manage to delete the file? (del b is not enough!).
All the best for 2022!
Eric
------------------------------
Subject: Digest Footer
_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org
https://mail.python.org/mailman/listinfo/neuroimaging
------------------------------
End of Neuroimaging Digest, Vol 80, Issue 3
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From arokem at uw.edu Wed Jan 19 20:56:51 2022
From: arokem at uw.edu (Ariel Rokem)
Date: Wed, 19 Jan 2022 17:56:51 -0800
Subject: [Neuroimaging] Fwd: Shanahan Foundation Fellowship at the Interface
of Data and Neuroscience - apply now!
In-Reply-To: <223D597E-BDDE-47DB-AEF2-12DF31EDADFE@uw.edu>
References: <223D597E-BDDE-47DB-AEF2-12DF31EDADFE@uw.edu>
Message-ID:
With apologies for cross-posting, this is a great opportunity at UW/Allen.
Please forward to potential applicants and note upcoming deadline.
Cheers,
Ariel
Overview
The *Shanahan Foundation Fellowship at the Interface of Data and
Neuroscience* is a three-year fellowship program that aims to:
? Integrate data scientists in neuroscience research
? Challenge traditional approaches to neuroscience
? Provide multidisciplinary, multi-organizational co-mentorship
? Provide a network and community
? Support career development in data science
The fellowship is co-hosted by the Allen Institute and the University of
Washington (through the eScience Institute and the Computational
Neuroscience Center) and is directed by Dr. Christof Koch at the Allen
Institute.
*Neuroscience needs data scientists.* The brain represents one of the most
complex challenges facing science today. And now with advances in our
methods to study the brain?Neuropixel probes that can record from 1000
neurons at once, growing consensus on data standards across
laboratories?the field is flooded with data that needs interpretation. The
skills of data scientists are essential to springboard the field to the
next stage of discoveries.
Towards that end, the Shanahan Foundation Fellowship was created to bring
fresh perspectives into the field, encouraging data scientists from outside
neuroscience to come and work with leading investigators at the Allen
Institute and UW.
The Allen Institute is unique in its infrastructure and pipeline that
enables the production of standardized, reproducible data on the brain (as
evidenced by our vast *data banks* *)*. Together
with our collaborators at the UW computational Neuroscience Center and
eScience Institute, we provide data scientists with the ideal opportunity
and resources to mine for novel insights and discoveries.
Details
*You do not need experience in neuroscience to apply. *The goal of the
fellowship is to provide opportunities to non-traditional applicants who
would not typically be funded by the typical postdoctoral fellowships in
neuroscience. The fellowship has been purposefully designed to give fellows
the time and mentorship to get up to speed in a new field and new data
collection techniques and methods*.*
Fellows will be employed by the Allen Institute as either a Scientist I or
a Scientist II (with a matching salary) and will receive an affiliate
postdoctoral appointment at UW.
During the three-year fellowship, fellows will identify a mentor at the
Allen Institute, where the fellows will be based. Fellows will select a
co-mentor at the University of Washington who will provide additional
guidance on a project designed by the fellow, focused on quantitative
analysis of neuroscience data available through the Allen Institute?s vast data
banks ? ranging from molecular, genomic,
transcriptional, physiological, morphological, anatomical and functional
whole-brain level in the brains of mice, non-human primates and humans ? or
through ongoing laboratory work. Each fellow will have the opportunity to
mentor a fully-funded UW undergraduate or postbaccalaureate research
assistant who helps with their research for 3-12 months.
Fellows will participate in the postdoctoral career development program at
the University?s *e-Science Institute* and the *UW Computational
Neuroscience Center*. The eSciences Institute offers regular workshops on
key topics including cloud computing, python and reproducibility. New
fellows will attend the annual Summer Workshop on the Dynamic Brain
where
they will learn how to apply data science skills to neuroscience data and
questions. Throughout the three years, fellows will be supported in
developing a network in the neuroscience field and sharing their progress
with peers at conferences. Up to three fellows will be selected to begin in
Fall 2022.
Eligibility Requirements
Applicants must be data scientists in a broad sense, with a Ph.D. in a
quantitative field such as computer science, statistics, electrical
engineering, physics, mathematics or biology with a background in
statistical, computational and machine learning methods. Ph.D.?s should
have been awarded in the last 3 years.
One goal of the fellowship is to build a network of collaborators, as such,
priority will be given to applicants who are not currently postdoctoral
fellows or scientists at the University of Washington or the Allen
Institute.
We believe high-quality science can only be produced when it includes
different perspectives. We are building an environment of diversity and
inclusion and encourage people from all backgrounds to apply for this
fellowship.
Application Instructions
For full consideration, please submit your application by February 1, 2022.
Applications may continue to be considered after this deadline on a rolling
basis until positions are filled.
Learn more and apply on the Shanahan Fellowship Website
.
https://alleninstitute.org/what-we-do/brain-science/careers/shanahan-foundation-fellowship/
Applications must include:
? A curriculum vitae from the applicant
? Two letters of support from advisors and other mentors
? A one-page personal statement from the applicant describing their
history, activities, and interests as an individual (especially those
outside of science) which may give the committee a greater sense of you as
a person and your ability to simultaneously interact with and challenge
traditional scientific fields.
? A two- to three-page research statement from the applicant
describing their prior research, interests in applying data science to the
field of neuroscience, potential research interests (including tools they
are familiar with) and how this fellowship aligns with their career goals.
? The choice of the final advisor/co-advisor will be accomplished
during the first year of this fellowship.
Questions? Email: shanahan.fellow at alleninstitute.org
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From pini.lorenzo2 at gmail.com Fri Jan 28 09:39:49 2022
From: pini.lorenzo2 at gmail.com (Lorenzo Pini)
Date: Fri, 28 Jan 2022 15:39:49 +0100
Subject: [Neuroimaging] Distance nipype
Message-ID:
Hi all,
I'm using Distance to compute some metrics between two images.
I saw the documentation and the scripts and I tried to run with the
following command:
Distance(self='/home/pnc/Desktop/PinNC_v5/test/T1w_control_005_2_brainFS.nii.gz',
volume1 = 'mydir/test/Image1.nii.gz',
volume2 = 'mydir/test/Image2.nii.gz',
method = "eucl_max")
res = Distance.run()
However, there is an error with the self function:
TypeError: run() missing 1 required positional argument: 'self'
and when I inspect the input I have the following:
mask_volume =
method = eucl_min
volume1 =
volume2 =
What's the problem here?
Thanks
L
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From arokem at uw.edu Fri Jan 28 09:54:55 2022
From: arokem at uw.edu (Ariel Rokem)
Date: Fri, 28 Jan 2022 06:54:55 -0800
Subject: [Neuroimaging] Distance nipype
In-Reply-To:
References:
Message-ID:
Hi Lorenzo,
Thanks for your email. Could you try the following?
my_dist =
Distance(self='/home/pnc/Desktop/PinNC_v5/test/T1w_control_005_2_brainFS.nii.gz',
volume1 = 'mydir/test/Image1.nii.gz',
volume2 = 'mydir/test/Image2.nii.gz',
method = "eucl_max")
res = my_dist.run()
To explain: in the code you sent, the error arises because you are calling
the `run` method on the class, and not an instance of the class. In the
code I provided above, I first create an instance of the class `Distance`
and then call the method from this instance.
Hope that helps,
Ariel
On Fri, Jan 28, 2022 at 6:40 AM Lorenzo Pini
wrote:
> Hi all,
>
> I'm using Distance to compute some metrics between two images.
> I saw the documentation and the scripts and I tried to run with the
> following command:
>
> Distance(self='/home/pnc/Desktop/PinNC_v5/test/T1w_control_005_2_brainFS.nii.gz',
> volume1 = 'mydir/test/Image1.nii.gz',
> volume2 = 'mydir/test/Image2.nii.gz',
> method = "eucl_max")
> res = Distance.run()
>
> However, there is an error with the self function:
> TypeError: run() missing 1 required positional argument: 'self'
>
> and when I inspect the input I have the following:
>
> mask_volume =
> method = eucl_min
> volume1 =
> volume2 =
>
> What's the problem here?
> Thanks
> L
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From pini.lorenzo2 at gmail.com Fri Jan 28 10:12:06 2022
From: pini.lorenzo2 at gmail.com (Lorenzo Pini)
Date: Fri, 28 Jan 2022 16:12:06 +0100
Subject: [Neuroimaging] Distance nipype
In-Reply-To:
References:
Message-ID:
Yes, It makes sense, sorry for my confusion.
Now I have "only" a memory issue with the data:
MemoryError: Unable to allocate 35.1 GiB for an array with shape (66897,
70517) and data type float64
Is it referring to the warning in metrics.py file? # there is a bug in
some scipy ndimage methods that gets tripped by memory mapped objects
Do you know how I can solve this?
Best,
L
Il giorno ven 28 gen 2022 alle ore 15:57 Ariel Rokem ha
scritto:
> Hi Lorenzo,
>
> Thanks for your email. Could you try the following?
>
> my_dist =
> Distance(self='/home/pnc/Desktop/PinNC_v5/test/T1w_control_005_2_brainFS.nii.gz',
> volume1 = 'mydir/test/Image1.nii.gz',
> volume2 = 'mydir/test/Image2.nii.gz',
> method = "eucl_max")
> res = my_dist.run()
>
> To explain: in the code you sent, the error arises because you are calling
> the `run` method on the class, and not an instance of the class. In the
> code I provided above, I first create an instance of the class `Distance`
> and then call the method from this instance.
>
> Hope that helps,
> Ariel
>
>
> On Fri, Jan 28, 2022 at 6:40 AM Lorenzo Pini
> wrote:
>
>> Hi all,
>>
>> I'm using Distance to compute some metrics between two images.
>> I saw the documentation and the scripts and I tried to run with the
>> following command:
>>
>> Distance(self='/home/pnc/Desktop/PinNC_v5/test/T1w_control_005_2_brainFS.nii.gz',
>> volume1 = 'mydir/test/Image1.nii.gz',
>> volume2 = 'mydir/test/Image2.nii.gz',
>> method = "eucl_max")
>> res = Distance.run()
>>
>> However, there is an error with the self function:
>> TypeError: run() missing 1 required positional argument: 'self'
>>
>> and when I inspect the input I have the following:
>>
>> mask_volume =
>> method = eucl_min
>> volume1 =
>> volume2 =
>>
>> What's the problem here?
>> Thanks
>> L
>> _______________________________________________
>> 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
>
--
*Lorenzo Pini, PhD *
*Padova Neuroscience Center, PNC*
Universit? degli Studi di Padova
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