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Re: [Freesurfer] CVS question
by Michael Zeineh 14 Jul '16

14 Jul '16

> Date: Thu, 14 Jul 2016 10:35:43 -0400 (EDT) > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] CVS question > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1607121530370.50358(a)semmelweis.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Michael, > >> I want to compare two populations using CVS so I can cross-register multimodal maps (e.g. ASL, FA, QSM) for volumetric comparisons. >> >> I?ve gotten CVS to work very well registering one subject to another, it really is impressive >> >> However, using the --mni option, it doesn?t work so well, perhaps because the atlas is so averaged together and smoothed out, the images look highly warped. >> >> I know I can pick a subject at random, and register everything to that, but that may induce some biases. The following website suggests I might try simply creating my own atlas (under the answers to Nov 2014 course questions):?https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAn… >> >> Seems like they register 40 subjects with each other for multiple iterations, average the brain together, then run recon-all on that. How does one actually do that, however? i.e. 1st round, register everyone to subject 1 ? then what? Seems like somehow you would want a registration intermediate point somehow? > > Have you tried to use the default cvs atlas? If you do not indicate any > explicit targets that is what will get used. I think that might be a > solution that you are looking for. > > Lilla > > ------------------------------ > Thank you, I happened to try that after I had sent this help request, and yes, it works much, much better. The transformation to MNI space is highly warped, that I realize was the problem. Thank you for your help.

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

14 Jul '16

The MAC version is now fixed as well. It should be available for download in the next couple of days (Zeke can provide a better estimate). Thanks again to all of you for your feedback. /E Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 14 Jul 2016, at 10:05, Fernando Pérez-García <fepegar(a)gmail.com<mailto:fepegar@gmail.com>> wrote: I am using Ubuntu 14.04.4. Please let me know if you need some more info. Cheers, Fernando 2016-07-14 10:59 GMT+02:00 Iglesias, Eugenio <e.iglesias(a)ucl.ac.uk<mailto:e.iglesias@ucl.ac.uk>>: 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://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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Measuring cortical thickness
by Dev vasu 14 Jul '16

14 Jul '16

Dear Sir / madam, I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I would like to know how could i generate cortical thickness maps for multi subject group analysis. The initial pre-processing with recon-all takes several hours for single subject, is there any alternate way to approach this problem in a limited amount of time?. Any help would be greatly appreciated. Thanks Vasudev

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CVS question
by Michael Zeineh 14 Jul '16

14 Jul '16

Hi, I want to compare two populations using CVS so I can cross-register multimodal maps (e.g. ASL, FA, QSM) for volumetric comparisons. I’ve gotten CVS to work very well registering one subject to another, it really is impressive However, using the --mni option, it doesn’t work so well, perhaps because the atlas is so averaged together and smoothed out, the images look highly warped. I know I can pick a subject at random, and register everything to that, but that may induce some biases. The following website suggests I might try simply creating my own atlas (under the answers to Nov 2014 course questions): https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers> Seems like they register 40 subjects with each other for multiple iterations, average the brain together, then run recon-all on that. How does one actually do that, however? i.e. 1st round, register everyone to subject 1 … then what? Seems like somehow you would want a registration intermediate point somehow? Any help would be great, thank you! Michael Zeineh, M.D.-Ph.D. Assistant Professor, Dept. of Radiology Stanford University Lucas Center for Imaging

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RB_all_2008-03-26.gca
by Gabor Perlaki 14 Jul '16

14 Jul '16

Dear all, Is it possible somehow to visually inspect the segmentations of the individual subjects used for the RB_all_2008-03-26.gca atlas? I can extract the means, priors and labels, but I am rather interested in the original MRI intensities and labels for the individual subjects. Best Regards, Gabor <petzinger.gabor(a)gmail.com>

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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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