Freesurfer

freesurfer@nmr.mgh.harvard.edu

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1-year position for an engineer to work in Parkinson, in the frontiers of imaging and machine learning (Bilbao, Spain)
by Iñigo Gabilondo 18 Sep '18

18 Sep '18

External Email - Use Caution We are looking for an Engineer with skills in computer vision, programming and machine learning to collaborate in the research project entitled: "Study of the retina and the visual pathway by neuroimaging in genetic and aggressive idiopathic synucleinopathies as a model to identify phenotypes and prognostic biomarkers in idiopathic Parkinson's disease" (Principal Investigator: Iñigo Gabilondo, MD, PhD) led by the Neurodegenerative Diseases Group. The data to analyse are multimodal and longitudinal, with a sample size bigger than N=100 and consisting in retina OCT, magnetic resonance imaging (structural, functional, tensor tensor and spectroscopy), neuropsychology and clinical scales. The engineer also will work in close collaboration with the Computational Neuroimaging Group, led by Prof. Jesus M Cortes. For further information about the groups, visit: https://biocrucesbizkaia.org/web/biocruces/bc5.01 and https://biocrucesbizkaia.org/bc5.08 Requirements: - Bachelor of Engineering - Good academic marks (average score higher than 7 over 10) - Experience in computer vision, programming (Matlab, Python and / or R), machine learning and other artificial intelligence techniques - Experience with the magnetic resonance imaging analysis packages SPM, FSL and Freesurfer - Advanced English level (demonstrable with official degree - C1) - Intention to develop a PhD in Biomedicine. The contract is for 1 year, but exists the possibility to extend it to finalize the PhD Working conditions: - Duration: 12 months (extendable) - Full working day (100%) (1592 annual hours) - Estimated annual gross salary: 23,004 euros per year - Expected start date: As soon as possible Interested candidates send 2 reference letters and updated CV to igabilon(a)gmail.com and/or jesus.m.cortes(a)gmail.com *Gurutzetako Unibertsitate Ospitalea /* *Hospital Universitario Cruces* *Plaza de Cruces 12 * *48903 – Barakaldo (Bizkaia)* *Iñigo Gabilondo Cuellar, MD PhD* Neurodegenerative Diseases Group *+34 946006000 <%2B34%20946006000> ext. 7970* igabilon(a)gmail.com INIGO.GABILONDOCUELLAR(a)osakidetza.eus *biocrucesbizkaia.org/web/biocruces/bc5.01 <http://biocrucesbizkaia.org/web/biocruces/bc5.01>*

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R: Freesurfer Digest, Vol 175, Issue 16________________problem with trac-preproc just at the middle of Priors point 2°
by marco.muti＠tin.it 18 Sep '18

18 Sep '18

External Email - Use Caution I tryed to run the elmo.2005 case in the administrator directory /usr/local with 23 GB free space, but the elaboration is stopped a little bit before the elaboration maded in a directory with 2 GB of free space.So I think is not a problem of memory, maybe could be a problem with the download of Freesurfer V 6.0, could you sand me the check sum link please? I can't find it. Anyway ....Thanks!!!! ----Messaggio originale---- Da: freesurfer-request(a)nmr.mgh.harvard.edu Data: 13-set-2018 17.48 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Freesurfer Digest, Vol 175, Issue 16 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: 6.0.1 automatic download (Chris Gorgolewski) 2. segmentation fault with mri_vol2vol or lta_convert (valabregue) 3. Re: Midline errors (Bruce Fischl) 4. Re: /mri/orig/001.mgz vs T1.mgz (Alexopoulos, Dimitrios) 5. Re: ??? questions about trac-all -stat (Yendiki, Anastasia) 6. Re: problem with trac-preproc just at the middle of Priors point (Yendiki, Anastasia) ---------------------------------------------------------------------- Message: 1 Date: Thu, 13 Sep 2018 07:38:19 -0400 From: Chris Gorgolewski <krzysztof.gorgolewski(a)gmail.com> Subject: Re: [Freesurfer] 6.0.1 automatic download To: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAAQzouPbjjqwEuTvVkgLzHQ5MMSoXrDXz4HEb7P5F9L04wAouQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thanks! Best, Chris PS Apologies for brevity and potential typos. This message was composed on a phone. On Wed, Sep 12, 2018, 5:06 PM Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote: > Hi Chris, that is the same version as before. Sorry, our pubftp disk went > down a few days ago and we had to restore some things manually (I guess the > original filename was copied). I renamed the tarball back to > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz > > > > best, > > Andrew > > > > > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Chris > Gorgolewski <krzysztof.gorgolewski(a)gmail.com> > *Reply-To: *FS Help <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Wednesday, September 12, 2018 at 11:03 AM > *To: *FS Help <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] 6.0.1 automatic download > > > > * External Email - Use Caution * > > Hi, > > > > I noticed that > > > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Lin… > > > is no longer available, but instead there is > > > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Lin… > > > > Is it the same thing or an updated version (if so why not 6.0.2)? Is this > the right way to grab the same 6.0.1 version in a programmatic way? > > > Best, > > Chris > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

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Flash nii to mgz failure
by Kambiz Tavabi 17 Sep '18

17 Sep '18

External Email - Use Caution Greetings, I am having trouble converting flash volumes (nii.gz) to mgz type using mri_convert. I used dcm2nii to unpack original DICOM files and subsequently the command mri_convert flash5.nii.gz flash5.mgz fails with... niiRead(): bad number of dimensions (-26421) Also, corresponding flash30.nii.gz conversion files with similar error: niiRead(): bad number of dimensions (25612). Any ideas what this error means? and how to resolve? ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-685-6173 ------------------------------------------------------------

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cross sectional hippocampal edits
by Rebecca Ray 17 Sep '18

17 Sep '18

External Email - Use Caution I am working on MRIs with a single time point. FreeSurfer appears to over estimate the hippocampus in 99% of the cases. I have attempted to correct the segmentation but after running autorecon2 and autorecon3 it did not make the changes that I made. How do I correct hippocampal overestimation? I would love your help. Best, Rebecca Ray

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Thalamic Nuclei segmentation
by Miguel Ángel Rivas Fernández 17 Sep '18

17 Sep '18

External Email - Use Caution Hi Freesurfer devs, Just a simple question, it´s possible make the thalamic nuclei segmentation using as input a simple T2 image as additional scan or by contrary, is always required use as input a more specific scan such as the FGATIR or a DBS scan. Best, -- *Miguel Ángel Rivas Fernández*

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is infant pipeline available in freesurfer?
by yuanchao.zhang8＠gmail.com 16 Sep '18

16 Sep '18

External Email - Use Caution Hi experts, I want to compare the morphological indice (such cortical thickness) between two groups of infants (age < 2), namely diseased group and a control group. I see that freesurfer cannot process MRI image of children smaller than 4 years. I am wondering if the infant pipeline available in freesurfer? I noticed that some one in freesurfer are developing such a pipeline. thanks a lot! Best, Yuanchao Zhang yuanchao.zhang8(a)gmail.com

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回复：回复： questions about trac-all -stat
by 薛倩雯 16 Sep '18

16 Sep '18

External Email - Use Caution Hi Yendiki, Anastasia, Thank you very much for your reply! I have two more question. (1)Even in the MNI space, the path positions of each subject could not be exactly coincident. So,how to identify the common midpoint for all subjects? (2)how to identify step size of the equally sized step you mentioned above? Thanks! Qianwen ------------------ 原始邮件 ------------------ 发件人: "Yendiki, Anastasia"<AYENDIKI(a)mgh.harvard.edu>; 发送时间: 2018年9月13日(星期四) 晚上11:44 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer]回复： questions about trac-all -stat Hi Qianwen, (1) & (2): The native space coordinates along the path of all subjects (which are in their path stats files) are mapped to MNI space simply to identify a common midpoint for all subjects. This midpoint is mapped back to native space, and the FA/MD/etc. values for each subject are sampled along the path by stepping out by equally sized steps from the midpoint towards both ends. At each step, you get one row of the group table. (3): Look for the paragraph "This text file contains various diffusion measures…” in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics And slide “Path stats (values along the path)” in the course slides: http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt Hope this helps, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of 薛倩雯 <627611631(a)qq.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 12, 2018 at 9:47 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] 回复： questions about trac-all -stat External Email - Use Caution Hi Yendiki, Anastasia, I am very sorry that I did not make myself clear. I mean I want to know how trac-all –stat does it. (1)how to determine the first position and last position of all subjects' pathways when converting all pathstats.byvoxel.txt files to a table for group analyses? In the tabel , The first position and last position of all subjects' pathways are determined by the longest pathway. (2)how to complete correspondence of points between subjects? In the course slides, it said"Correspondence of points between subjects based on Euclidean distance in MNI space".This sentence is so vague that I can't understand it. (3)what is values in table for group analyses,diffusion measure of center or something else? I am very sorry that my question is a bit more, but I still hope that you can answer my doubts. Thanks! Qianwen ------------------ 原始邮件 ------------------ 发件人: "Yendiki, Anastasia"<AYENDIKI(a)mgh.harvard.edu>; 发送时间: 2018年9月12日(星期三) 晚上10:40 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] questions about trac-all -stat Hi Qianwen – You don’t have to do (1) and (2), trac-all –stat does that for you. For a description of the measures, see the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics and the course slides: http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of 薛倩雯 <627611631(a)qq.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 12, 2018 at 1:13 AM To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] questions about trac-all -stat External Email - Use Caution Dear experts, I have some questions about along-path analysis: (1)how to determine the first position and last position of all subjects' pathway when converting all pathstats.byvoxel.txt files to a table for group analyses? (2)how to complete correspondence of points between subjects? (3)what is values in table for group analyses,diffusion measure of center or something else? Thanks! Qianwen

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Download and Registration issue
by Juliane Corlier 16 Sep '18

16 Sep '18

External Email - Use Caution Dear list, I have to issues: 1) I am trying to download a dmg installer file for Freesurfer from this website: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall <https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall> I get an error that the page is not working/can’t be opened. 2) I am trying to set up an account via the new registration link, but I get an error code saying “You are not allowed to do newaccount on this page. Login and try again.” Please let me know if those are only temporary problems or how could I resolve them. Thank you, Juliana

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FS-FAST and thalami nuclei
by stdp82＠virgilio.it 16 Sep '18

16 Sep '18

External Email - Use Caution Hi list, I would like to use as seed the output of segmentation of the thalamic nuclei in FS-FAST. Probably some nuclei may be too small to be used as seed. Are you agree? I wonder if to merge the outputs in 5-10 subregions (e.g. AV, MD, MC etc...) could be the most appropriate way. What do you advise? Thanks Stefano

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Overlay electric field distribution on pial surface
by Meusen - Klooster, D.C.W. 15 Sep '18

15 Sep '18

External Email - Use Caution Dear all, I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my other images. I have a .nii file of the electric field distribution, registered to T1, representing field strengths in every voxel. Visualization in freeview looks okay, but visualization using tksurfer does not really give the right results (most of the brain is yellow... no field distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how to accomplish this? Thank you very much in advance. Best, Debby

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