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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 https://mail.python.org/mailman/listinfo/neuroimaging or, via email, send a message with subject or body 'help' to neuroimaging-request at python.org You can reach the person managing the list at neuroimaging-owner at python.org 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 ******************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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