Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?
by Iglesias, Eugenio 14 Jul '16

14 Jul '16

Dear Fernando, Are you using the MAC version? I haven’t finished fixing the bugs in that one yet. If you’re using the Linux version: Zeke, can you please shed some light on what the problem might be? Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 14 Jul 2016, at 08:57, Fernando Pérez-García <fepegar(a)gmail.com<mailto:fepegar@gmail.com>> wrote: Dear Eugenio, I'm still having this issue, even after downloading the latest development version from the website as you suggested. My steps (yesterday): 1. Download and install FS (dev version) 2. Run recon-all 3. Download and install Matlab runtime 4. Run recon-all with brainstem structures I get the following error: Error:Cannot find CTF archive /usr/local/freesurfer/bin/SegmentSubject.bin.ctf Should I try the same steps again today? Best, Fernando

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how to calculate total pial surface area?
by Mihaela Stefan 13 Jul '16

13 Jul '16

Hello Freesurfers, We would like to know how to calculate the total pial surface area for each hemisphere. We extracted the surface area from the 34 ROIs per hemi from lh.aparc.stats but there is no total pial surface area in that file (only white surface area). Does it make sense to just add the 34 ROIs or there's a better way to extract that measure? Thanks! Mihaela

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question about white matter edits
by Ritobrato Datta 13 Jul '16

13 Jul '16

Hi All, We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows recon-all -autorecon2-cp -autorecon3 -subjid <subject> but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ? Can someone please suggest ? Thank you, Rito and Jack

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Post-doctoral position at MRC Cognition and Brain Sciences Unit
by Tibor Auer 13 Jul '16

13 Jul '16

MRC Cognition and Brain Sciences Unit - Cambridge Postdoctoral Scientist Salary £27,355 - £30,791 per annum plus benefits Ref OH/260 The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally renowned research institute of cognitive neuroscience. Onsite facilities include dedicated MRI and MEG scanners, a hearing laboratory, and the developmental research centre suitable for infants through to older children. The CBSU is also a stakeholder in a clinical research facility and a new 7T ultra high field MRI scanner on the Addenbrooke's campus in Cambridge. An open-ended post-doctoral position is available in the Methods Team to support the optimisation, standardisation and development of fMRI data analysis pipelines, e.g. for standard fMRI time series analysis, functional and effective connectivity analysis, and multivariate pattern analysis. Methods support may extend to EEG/MEG analysis where appropriate. The successful candidate will also participate in a skills-oriented neuroimaging training programme aimed at PhD students and post-doctoral researchers. The position offers scope for independent research and methods development. You will have, or be in the final stages of, a PhD related to physics, signal processing, or neuroimaging methods. You should have experience in fMRI analysis, scientific computing (e.g. Linux, Matlab, Python), and an appreciation of methodological issues in cognitive brain imaging. Experience with MRI data acquisition and EEG and MEG methodology would be desirable. You will be thorough, efficient, effective, a good communicator, and enjoy working as part of a diverse and energetic, interdisciplinary team. Choosing to come to work at the MRC CBSU means that you will have access to a whole host of benefits from a final salary pension scheme, 30 days annual leave entitlement, flexible working arrangements, childcare vouchers, and additionally a salary sacrifice cycle scheme, as well as access to employee/shopping travel discounts. On site car and bicycle parking is available. We also provide a wide range of training opportunities to all our staff. Our success is dependent on our ability to embrace diversity and draw on the skills, understanding and experience of all our staff. As holders of an Athena SWAN bronze award we welcome applications from all sections of the community irrespective of gender, race, ethnic or national origin, religion or belief, sexual orientation, disability or age. As users of the "Two Ticks" disability symbol we guarantee to interview all applicants with disabilities who meet the minimum essential criteria for the post. For full details of this post and to complete an online application form visit https://mrc.tal.net/vx/lang-en-GB/appcentre-1/candidate/postings/280 and upload your CV along with a covering letter stating why you are applying for the post. Closing date: 9th August 2016 [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> This position is subject to pre-employment screening The Medical Research Council is an Equal Opportunities Employer Auer, Tibor M.D. Ph.D. MRC Cognition and Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF United Kingdom Phone/Work: +44-(0)1223-273613 Mail: Tibor.Auer(a)mrc-cbu.cam.ac.uk<mailto:Tibor.Auer@mrc-cbu.cam.ac.uk>

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request for newer mri_tessellate (error: max vertices 1000000 exceeded)
by Ferguson, B. 13 Jul '16

13 Jul '16

Dear Freesurfer team, I am running Falk Luesebrinks hires recon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>, and am running into the error of "mri_tessellate: max vertices 1000000 exceeded" when I run the command line "recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT" on a 0.5mm T1 structural volume. I have seen an earlier e-mail conversation<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42045.html>, and would like to request: is a similar mri_tesselate that is easier about the number of vertices available for my platform? FREESURFER_HOME = /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Mac version: OS X Yosemite 10.10.5 Kernel info: Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 Thanks in advance, best wishes, Bart Ferguson PhD candidate | Department of Psychiatry | Brain Division | University Medical Center Utrecht Post: A01.126 kantoortuin 1 | Visit: A01.504| Heidelberglaan 100 | 3584 CG UTRECHT T +31 (0)88 75 555 55 | M +31 (0)6 1191 6897 | www.umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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post-doctoral position at MRC Cognition and Brain Sciences Unit, Cambridge
by Olaf Hauk 13 Jul '16

13 Jul '16

MRC Cognition and Brain Sciences Unit - Cambridge Postdoctoral Scientist Salary £27,355 - £30,791 per annum plus benefits Ref OH/260 The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally renowned research institute of cognitive neuroscience. Onsite facilities include dedicated MRI and MEG scanners, a hearing laboratory, and the developmental research centre suitable for infants through to older children. The CBSU is also a stakeholder in a clinical research facility and a new 7T ultra high field MRI scanner on the Addenbrooke's campus in Cambridge. An open-ended post-doctoral position is available in the Methods Team to support the optimisation, standardisation and development of fMRI data analysis pipelines, e.g. for standard fMRI time series analysis, functional and effective connectivity analysis, and multivariate pattern analysis. Methods support may extend to EEG/MEG analysis where appropriate. The successful candidate will also participate in a skills-oriented neuroimaging training programme aimed at PhD students and post-doctoral researchers. The position offers scope for independent research and methods development. You will have, or be in the final stages of, a PhD related to physics, signal processing, or neuroimaging methods. You should have experience in fMRI analysis, scientific computing (e.g. Linux, Matlab, Python), and an appreciation of methodological issues in cognitive brain imaging. Experience with MRI data acquisition and EEG and MEG methodology would be desirable. You will be thorough, efficient, effective, a good communicator, and enjoy working as part of a diverse and energetic, interdisciplinary team. Choosing to come to work at the MRC CBSU means that you will have access to a whole host of benefits from a final salary pension scheme, 30 days annual leave entitlement, flexible working arrangements, childcare vouchers, and additionally a salary sacrifice cycle scheme, as well as access to employee/shopping travel discounts. On site car and bicycle parking is available. We also provide a wide range of training opportunities to all our staff. Our success is dependent on our ability to embrace diversity and draw on the skills, understanding and experience of all our staff. As holders of an Athena SWAN bronze award we welcome applications from all sections of the community irrespective of gender, race, ethnic or national origin, religion or belief, sexual orientation, disability or age. As users of the "Two Ticks" disability symbol we guarantee to interview all applicants with disabilities who meet the minimum essential criteria for the post. For full details of this post and to complete an online application form visit https://mrc.tal.net/vx/lang-en-GB/appcentre-1/candidate/postings/280 and upload your CV along with a covering letter stating why you are applying for the post. Closing date: 9th August 2016 [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> [https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcS606DGyDyDGODetutPc9b…] <http://www.google.co.uk/imgres?sa=X&biw=1920&bih=847&tbm=isch&tbnid=1eBdQ7E…> This position is subject to pre-employment screening The Medical Research Council is an Equal Opportunities Employer Olaf Hauk, PhD MRC Cognition and Brain Sciences Unit Phone: +44(0)1223 273702 Fax: +44(0)1223 359062 Web: http://www.mrc-cbu.cam.ac.uk/people/olaf.hauk/

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TRACULA tract group comparison p-values
by Barbara Kreilkamp 13 Jul '16

13 Jul '16

Dear Freesurfers, I am looking for a way to add a colorbar to my p-value tract cores generated through TRACULA. When I load up the images as described in the tutorial here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and there is no option to select my textfile with the p-values unfortunately. Would you please help? Thanks ever so, Barbara

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FreesurferNHP
by Lauro, Peter 12 Jul '16

12 Jul '16

Hello, I'm trying to reconstruct cortical surfaces from non-human primate MRIs. I tried following the instructions/scripts listed here ( https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData) but I was unable to make it work (I'm also running FS 5.3). I noticed on the Washington-Pipelines github FAQ page listed a FreesurferNHP pipeline ( https://github.com/Washington-University/Pipelines/wiki/FAQ#9-what-if-i-wan…) but it hasn't been released yet. Do you know when this pipeline will be available? Alternatively, is there another way I can obtain the pipeline scripts and template volumes? Thank you, Pete Lauro

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ERROR reading /..../label/lh.BA1.label
by Uquillas, Federico D'Oleire 12 Jul '16

12 Jul '16

Dear fellow FreeSurfer users, My jobs fail at the the last mri_label2label step of -autorecon3, and I cannot figure out why. Any help or input would be greatly appreciated. I am attaching a recon-all log for two of these subjects. The error says that it's not possible to read the labels contained in the fsaverage/labels/ folder. These labels/files do exist however if you look in the /labels/ folder. I'm using Centos 6.7 (Final) Kernel Linux 2.6.32-573.22.1.el6.x86_64 GNOME 2.28.2 My username is fdu0. A path to my most recent error fail can be the following: /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 (PBS Job ID: 11918069) another one with this same error fail is /FreeSurferProc/AD08 (PBS Job ID: 11914847). Thank you very much for your time and any help you may be able to provide. Fred

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Fwd: TRACULA stat extraction issue
by Shashwath Meda 12 Jul '16

12 Jul '16

Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation? tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table -- Best, Shashwath

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Freesurfer July 2016