Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

Hippocampal subfield segmentation problem
by Artyom Zinchenko 22 May '17

22 May '17

Dear experts, I am running running hippocampal subfield segmentation using the most recent version of the FSv6.0 on LinuxMint 17.3 Rosa. For some (~ 25%, but not all) participants I did not get the subfields. I have later realized that although segmentation finished with out errors, I got the following message in the end: Error using kvlGEMSMatlab std: :bad_alloc Error in kvlRasterizeAtlasMesh (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 628). I have read that I need to check whether the T1resampled.mgz actually exists in the temporary directory of the subject. I have checked and this file is indeed there: SBJ/tmp/hippoSF_T1_v10_right/T1resampled.mgz. Please, let me know if this is a known problem and if there is anything I can do to correct it? Thank you very much in advance, Artyom

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wmsubseg and hippocampal subfield in gtmseg
by Chakmeedaj Sethanandha 22 May '17

22 May '17

Dear Freesurfer Experts, We have experiment on functional change based on PET in white matter and found that freesurfer's gtmpvc is very much helpful. We would like to ask if we can get gtmseg to subsegment wm in to gyral based parcellation instead of lobar wm? We know that we can create our own segmentation based on wmparc.mgz but it would be better to have a more automate way. On this matter, we also would like to add hippocampal subfield as segmented by "-hippocampal-subfields-T1" in recon-all for gtmseg results. Will this be allowed? Best, Jak

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-usegpu vs -parallel in recon-all
by Octavian Lie 20 May '17

20 May '17

Dear All, With FS6, -parallel -openmp x can really speed things up. I inherited code from prior versions using -usegpu flag for GPU/CUDA (not supported more recently). Is the latter redundant or affecting in any way the -parallel -openmp x performance, should we take it out, please advise. Thank you, Octavian

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Cuda 8, Centos 7, FreeSurfer 6
by neuroimage analyst 20 May '17

20 May '17

Hello. We recently installed Centos 7 with cuda 8 and tried to build the FreeSurfer 6.0 using the wiki instructions but were unsuccessful to do so. Has anyone successfully built FreeSurfer 6 on Cuda 8 (Centos 7) and willing to share the binaries with us or share their steps with us? We will greatly appreciate that. Thanks Regards V

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ERROR: nu_correct
by Das S. 20 May '17

20 May '17

Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 When I executed the command separately I got below error message: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani

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Re: [Freesurfer] Manuel edits (message 5)
by Caroline Beelen 19 May '17

19 May '17

Dear Bruce, Thank you for answering my question. However, I'm still in a bit confused... Therefore, I have one more question: Would it then be best to choose a particular WM intensity value to rely upon for adding control points or to rely upon sight? Thank you very much! Kind regards, Caroline Beelen -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request(a)nmr.mgh.harvard.edu Verzonden: donderdag 18 mei 2017 18:00 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 159, Issue 31 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. Postdoctoral position in psychosis studies - Oslo, Norway (Tiril Pedersen Gurholt) 2. manuel edits (Caroline Beelen) 3. Re: Question of longitudinal processing (jahanvi patel) 4. Re: Mean gray-white contrast for each ROI (Douglas N Greve) 5. Re: manuel edits (Bruce Fischl) 6. Re: Freesurfer white matter outer edge to volume (Douglas N Greve) 7. Re: mri_mcsim for individual subjects and references {Disarmed} (Douglas N Greve) 8. Improving the brainmask.mgz using aseg.mgz for getting rid of dura (Karteek Popuri) 9. Re: Improving the brainmask.mgz using aseg.mgz for getting rid of dura (Douglas N Greve) 10. Re: Improving the brainmask.mgz using aseg.mgz for getting rid of dura (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Thu, 18 May 2017 12:04:49 +0000 From: Tiril Pedersen Gurholt <t.p.gurholt(a)medisin.uio.no> Subject: [Freesurfer] Postdoctoral position in psychosis studies - Oslo, Norway To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9E8A081E-D148-4B08-B276-DD5B58C20E93(a)medisin.uio.no> Content-Type: text/plain; charset="utf-8" Dear All, At the NORMENT ? K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital and Diakonhjemmet Hospital, Norway, there is a position available as a postdoctoral student with employment at Diakonhjemmet hospital. The research area is psychiatric neuroimaging with focus on obstetric complications and the analysis of structural and functional, DTI and ASL MR imaging datasets with regard to developmental trajectories and genetic, environmental and phenotypic variation. Applicants should have a doctoral degree (PhD) in psychiatry or a related medical discipline, neuroimaging, computer science, bioinformatics, psychology, or equivalent. Applicants who have handed in their dissertation for evaluation are also encouraged to apply, caveat the dissertation is approved. Application deadline is June 15th, 2017. For further information and to submit an application please see the website of Diakonh jemmet H ospital, Oslo, Norway: https://www.webcruiter.no/WcMain/advertviewpublic.aspx?oppdragsnr=342027797… Best regards, Tiril Gurholt --- Tiril Gurholt Postdoctoral Fellow Psychosis Research Centre, NORMENT Institute of Clinical Medicine, University of Oslo, Norway http://www.med.uio.no/norment/ [cid:image001.png@01D21DA0.544E82D0]

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Corrupted file (Matlab runtime 2012b Linux) on server?
by Marco Bucci 19 May '17

19 May '17

Hi all, I tried on a Linux server with Debian (also as sudo) curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do…" -o "runtime2012b.tar.gz" The transfer stops at about two minutes from the end. I tried to download the file manually from the website on a Mac, the transfer stops at 195 MB and does not finish, then timeout. Is it possible you have a corrupted file on the server at the moment? Can you help me? Best regards, Marco P.S. Also my colleague tried separately to download and the problem was still present. -- **************************************************** Marco Bucci, PhD in Clinical Physiology and Nuclear Medicine Turku PET Centre Turku University Central Hospital (TUCH) PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland tel. +358 2 3132798 fax. +358 2 2318191 mobile: +358 40 6873976 UTU e-mail: marbuc(a)utu.fi ****************************************************

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Grey matter misclassified as white matter
by Maryam Kouchakidivkolaei 18 May '17

18 May '17

Dear experts, I am using freesurfer V5.3. I am trying to fix some error in freesurfer outputs. The issue is that grey matter misclassified as white matter in temporal lobe (lh). I tried to edit Wm.mgz and re-run with -autorecon2-wm, but it did not work. Looking at the brainmask.mgz, white matter boundary includes area with intensity normalization less than 60-50. Any suggestion? I appreciate any help, Maryam

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help
by Aditya P Singh 18 May '17

18 May '17

> On May 18, 2017, at 11:29 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > 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: Freesurfer white matter outer edge to volume (Gamaliz) > 2. Re: Freesurfer white matter outer edge to volume (Gamaliz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 18 May 2017 12:16:46 -0400 > From: Gamaliz <gliza002(a)fiu.edu> > Subject: Re: [Freesurfer] Freesurfer white matter outer edge to volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CALei8e7=HH+Y8DoHLgUDLOci2BOrceA6b8XqqASSteMnN_AX+w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Douglas, > > I am looking at them in freeview and mango. They are not aligned. I am able > to align them using flirt, and they come out perfect. I have tried 5 cases. > 3 of them they are aligned, two were not. I am loading below the wm and > lh.wm. They are supposed to be aligned (wm is aligned with T1). > > I got a surface by using Bruce's method, but it's much more irregular than > the one obtained from mri_surf2vol. I wonder why the inconsistency. I guess > I can create the surface and flirt using a solid transform to the T1. It > takes longer, but it works. > > Gabriel > > [image: Inline image 1] >

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Questions about FreeSurfer
by Alliey-Rodriguez, Ney [PSY] 18 May '17

18 May '17

Dear FreeSurfers, I received FreeSurfer structural MRI brain data to analyze, but there are some questions about specific FreeSurfer variables that I could not find answered on your wiki or in the mail archive: 1.- "Non-White Matter hypointensities": 1.a - Are these the same thing as "gray matter hyperintensities"? 1.b - Are these scanned from the whole brain gray matter or only sub-cortical? 1.c - Are these also considered traumatic markers? (literature would be appreciated) 2.- 5th Ventricle: is this variable encompassing the Cavum Septum Pellucidum only, or does it also include the Cavum Vergae? 3.- Are there published analysis about FreeSurfer accuracy for CSF volumes? Thanks and will look forward, Ney __________________________ Ney Alliey-Rodriguez, M.D. Research Assistant Professor - Gershon Lab Department of Psychiatry and Behavioral Neuroscience University of Chicago 5841 S Maryland Ave Room M344 (MC3077) Chicago, IL 60637 Phone: 1(773)702-0599

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Freesurfer May 2017