Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

postdoctoral Fellowship for Child Brain Connectome and Genetics
by Anqi Qiu 19 Sep '18

19 Sep '18

External Email - Use Caution Job description: Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort study over the world. The GUSTO mothers were recruited during pregnancy between 2009 and 2010. We have followed the GUSTO family since then. The GUSTO study collects the unique data on cognitive functions, children behaviors, psychopathology, and brain imaging at multiple points from birth to 7 years of age. We aim to study whether mothers mood, diet, and family lifestyle since pregnancy affect 1) their babies cognitive and brain development; 2) psychopathology later in life. We also aim to examine the role of genetics in such maternal influences. We are looking for postdoctoral fellows who are interested in the GUSTO study. Requirements: 1. PHD in Cognitive Neuroscience, or Psychology, or Imaging Genetics; 2. Experience with MRI-based neuroimage techniques; 3. Knowledge in statistical analysis is necessary; 4. Good communication and writing skills in English language; 5. Knowledge in longitudinal analysis will be plus plus. If you are interested in the jobs listed above, please send your CV to Deans Chair, Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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postdoctoral Fellowship for Child Brain Connectome and Genetics
by Anqi Qiu 19 Sep '18

19 Sep '18

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Re: [Freesurfer] Surface Area in Toddlers/Children
by Douglas Greve 18 Sep '18

18 Sep '18

The flag to preserve area is not being turned on there. You can try running mris_preproc separately for area and including the --jac flag. If that does not work, you can download version6 and just use it to run mris_preproc On 8/10/18 4:41 PM, Derek Sayre Andrews wrote: > > External Email - Use Caution > > Hi Douglas, > > Of course, please find attached a copy of the recon-all.log file. > > Best, Derek > > PS: Apologies for the direct email in order to get you the attachment > > cid:image001.png@01D430A0.A5153C80 > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas > Greve <dgreve(a)mgh.harvard.edu> > *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Friday, August 10, 2018 at 11:12 AM > *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children > > Yes. -qcache actually calls mris_preproc. At one point, FS did not > preserve total area when mapping to fsaverage. I fixed it a while > ago, but maybe something was still off in 5.1 > > On 8/10/18 2:06 PM, Derek Sayre Andrews wrote: > > * External Email - Use Caution * > > Hi Douglas, > > Thank you for the response. > > I did not use mris_preproc to prepared the data. > > The data was mapped to fsaverage using recon-all with -qcache. I > then loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into > MATLAB using SurfStatReadData > <http://www.math.mcgill.ca/keith/surfstat/> and summed them across > each vertex. > > Would the terminal output of recon-all -qcache be helpful? > > Best, Derek > > cid:part2.2B5BCEFF.1D6DDEE5@mgh.harvard.edu > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of > Douglas Greve <dgreve(a)mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> > *Reply-To: *Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, August 10, 2018 at 10:25 AM > *To: *"freesurfer(a)nmr.mgh.harvard.edu" > <mailto:freesurfer@nmr.mgh.harvard.edu> > <freesurfer(a)nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children > > It should be preserving total surface area. Can you send your > mris_preproc command line and the terminal output? It might be > something with 5.1 as well. > > > > On 8/9/18 3:49 PM, Derek Sayre Andrews wrote: > > * External Email - Use Caution * > > Dear Freesurfer Developers and Experts, > > I have been exploring various vertex wise (mass univariate) > effects using freesurfer measures of cortical thickness and > surface area in a cohort of toddlers/children aged 25-70 months. > > When looking at the effect of age on surface area using > individuals’ measures mapped to fsaverage and smoothed at 15mm > fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread > negative effect of age (i.e. decreased surface area with age). > Given the age group of the cohort this seems implausible. > Plotting the sum of each individuals > lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the > relationship: > > cid:image001.png@01D42FCE.C197B360 > > However, plotting the lh+rh total surface area returned by > mris_anatomical_stats reveals a much more plausible > relationship between surface area and age: > > cid:image002.png@01D42FCE.C197B360 > > My working hypothesis is that the significantly smaller brain > sizes of our cohort compared to fsaverage, and the fact(?) > that -qcache does not preserve global surface area, is causing > an “over adjustment” in our cohorts smallest brains when > mapped to fsaverage. > > Thus, my questions are three fold > > 1. Is the mapping of our significantly smaller brains to > fsaverage a potential explanation for the results we are > seeing in our mass univariate analyses of surface area? > > 2. If this is the case, would this effect be limited to > surface area or also extend to other freesurfer measures > including cortical thickness, lGI, sulcal depth etc. > > 3. How would you recommend approaching vertex wise analyses > in a cohort of this age? Create a study specific average > subject using make_average_subject to map onto? > > Thank you for your insight and guidance! > > Best, Derek > > PS: All processing was performed using freesurfer v5.1 > > cid:image003.png@01D42FCE.C197B360 > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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T2pial correction options
by Adam Martersteck 18 Sep '18

18 Sep '18

External Email - Use Caution Hi Freesurfer team, We’re having some trouble with the T2pial option. We are currently getting the Martinos Center ABCD project Tisdall/van der Kouwe vNav MPRAGE and T2SPACE at 0.8mm^3, bandwidth matched for distortion. Linked below are 2 gifs were we have found areas we thought the T2 and –T2pial option would help differentiate brain from non-brain: https://goo.gl/dc9pjj https://goo.gl/AsCCbA I’ve read the discussion by Bruce, Matt, and Antonin about altering the final lh/rh mris_make_surface command with the T2. Has anyone found more optimal numbers for the nsigma_above and nsigma_below arguments? Is there anything else I could try to get this working better? Thanks! -Adam

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mris_register problem
by Chris Adamson 18 Sep '18

18 Sep '18

External Email - Use Caution Freesurfer experts, I'm having an issue with projecting labels from an atlas to a subject. I have a static annot file on the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register my subject to the atlas and then mri_surf2surf on the annot file using the registered spherical surfaces. The labels, when painted, are incorrectly oriented. How can I debug the output of the registration to check if the registration is working? I assume the registration works in the 2D parameterised space, can I extract parameterised versions of the curvature maps at each iteration of the registration. The strange thing is that when I view the spherical surfaces in freeview with the overlaid curvature maps they look in alignment prior to registration, but using this unregistered sphere still puts the labels in an incorrect orientation. So it appears as if there is some rotation that is being done internally that isn't shown in freeview. Please advise, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email

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How the resolution requirement was determined
by 조성현 18 Sep '18

18 Sep '18

External Email - Use Caution Hello Freesurfer developers and subscribers, I'm attempting to run brain segmentation with low resolution mri(thickness ~= 7mm) for EEG analysis. I know that this is very low resolution to get good quality results. However, I think the low quality result is not meaningless in specific cases. Therefore, I wonder if there is a tool to evaluate how low quality results are. In the 'freesurfer beginners guide', it says 'Thickness should not exceed 1.5mm'. How the resolution requirement was determined? How did you know that the input of 1mm ^ 3 resolution is sufficient requirement? If I use 2mm^3 resolution input, what kind of result will I get? It may be a little dumb, but I do not have an answer of this question. I would appreciate your reply. Thanks, Jo

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Questions on multiple inputs
by limiyu 18 Sep '18

18 Sep '18

External Email - Use Caution Dear developers I have a question on how could I segment two registered MRI images and get only one segmentation result, by command recon-all ? In details, I have two MRI images which are T1-weighted and T2-weighted. They are the photos of one brain. How could I input both of them into Freesufer and output one segmentation result, which takes both of the input into consideration. I know that command "recon-all -all" could output the segmentation but do not know what to do when there are multiple inputs. Looking forward to your reply Thank you Mingyuan Liu

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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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Freesurfer September 2018