Freesurfer

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NIMH-Sponsored Postdoctoral Fellowships in Traumatic Stress Disorders
by Emma Brown 07 Oct '19

07 Oct '19

External Email - Use Caution Collaborating research groups at the VA Boston Healthcare System anticipate up to two NIMH-funded postdoctoral fellowships to begin by September 3, 2020. These training positions are designed to prepare researchers for academically-oriented careers in the psychology and neurobiology of stress-related disorders. Previous fellows have launched successful careers in universities and academic medical settings. Candidates with backgrounds in neuroimaging and/or genetics are encouraged to apply. The fellowship program is affiliated with Boston University School of Medicine and is located primarily at the Jamaica Plain Campus of VA Boston. Affiliated centers include the Behavioral Science and Women's Health Sciences divisions of the National Center for PTSD, the Translational Research Center for TBI and Stress Disorders, the Neuroimaging Research for Veterans Center, and the Center for Healthcare Organization and Implementation Research. These programs offer outstanding resources including existing datasets, technical support personnel, well-equipped laboratories, advanced computing facilities, and a broad range of professional expertise. The anticipated salary and benefits package is competitive, and supplemental funds will be available to support further coursework and other educational opportunities, conference attendance, and travel. The program offers training in several core areas. Candidates may contact the following program leaders prior to application for more information about the specific cores: *Clinical Neuroscience and Neuroimaging*(David Salat salat(a)nmr.mgh.harvard.edu),*Molecular Biomarkers and Genetics*(Mark Miller: mark.miller5(a)va.gov) *Assessment, Diagnosis, and Epidemiology*(Brian Marx: brian.marx(a)va.gov) *Treatment Development and Optimization*(Denise Sloan: denise.sloan(a)va.gov) and *Implementation and Dissemination*(Katherine Iverson: katherine.iverson(a)va.gov) Fellows will havethe opportunity to participate in ongoing research projects conducted by program faculty, initiate independent research projects, conduct secondary analyses on existing data sets, prepare grant applications to federal and other funding agencies, and learn about all aspects of laboratory management. Each fellow will have a senior faculty member assigned to serve as a primary mentor. For license-eligible clinical psychology fellows, arrangements are available outside the program to provide direct clinical services to patients under the guidance of a clinical supervisor. *Materials will be reviewed and interviews arranged on a first-come basis. *Preliminary applications should include a statement of interests and goals, a curriculum vita, and three professional references that should be sent directly by the recommendation writer. *Applicants must be U.S. Citizens and have completed all requirements for their doctoral degree prior to starting the program*. Minority candidates are strongly encouraged to apply. Applications should be submitted electronically no later than December 2, 2019 to Denise Sloan, Ph.D. (*denise.sloan(a)va.gov <denise.sloan(a)va.gov>*). The VA Boston Healthcare System is an equal opportunity employer.

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retinotopy_receptive fields_ STIM PARAMETER
by Marco 07 Oct '19

07 Oct '19

External Email - Use Caution Dear experts, I am performing some study on visual receptive fields (using retinotopy stimuli) and have already run the -recon-all command and it worked fine. After that, I cut the occipital poles (left and right) and flattenend the results. So, now I have the flat patches images. I would like to use the retinotopy parameter file (now is a .mat file) in freesurfer (I found that should be something like a .par format? I don't know so well this format), so that would be possible for me to read it on freesurfer and proceed further on pipeline. How to achieve this step? Sorry if the question may results confusing. Thank you for your help, Marco -- ------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Re: [Freesurfer] Freeview PETSC errors (freeview doesn't start at all)
by fsbuild 06 Oct '19

06 Oct '19

External Email - Use Caution Hello Mohammad, Please tell us what version of linux you are running, e.g., Ubuntu 18, CentOS 7, etc. - R. Mohammad Rashid October 6, 2019 at 17:15         External Email - Use Caution         Hello all, I've looked through the archives extensively but I haven't seen any instances of these particular errors, which I get upon simply typing "freeview" into my console and hitting enter. Note that tksurfer for example does work. I'm on Linux and am using FreeSurfer v6.0.0. Here are all the error messages: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named PC by MR  Sun Oct  6 15:45:57 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3..3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Any help is appreciated. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview PETSC errors (freeview doesn't start at all)
by Mohammad Rashid 06 Oct '19

06 Oct '19

External Email - Use Caution Hello all, I've looked through the archives extensively but I haven't seen any instances of these particular errors, which I get upon simply typing "freeview" into my console and hitting enter. Note that tksurfer for example does work. I'm on Linux and am using FreeSurfer v6.0.0. Here are all the error messages: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named PC by MR Sun Oct 6 15:45:57 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Any help is appreciated.

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ECC or non-ECC Memory?
by Sotiris Michos 06 Oct '19

06 Oct '19

External Email - Use Caution Dear Freesurfer community, I am interested in building a PC with the goal of running Freesurfer (about 2000-2500 Euros). I have carefully read this <https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements> very informative webpage. However, I still have some questions and I would be glad if some assistance could be provided. I suspect that a proper PC would be placed towards the workstation side of the spectrum, since from what I read in the above webpage, Freesurfer can utilize multiple cores and is quite demanding in RAM memory per instance. What I would like to ask is whether ECC Memory is critical for this application or if the corruption coming from a non-ECC module has any significant effect on the end result. Also, any advice or suggestions about the system's buildup would be more than welcome. Best Regards, Sotiris Michos

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Re: [Freesurfer] Errors running TRACULA (data attached) - valid frame numbers
by Mazzetti, C. (Cecilia) 06 Oct '19

06 Oct '19

External Email - Use Caution Hi Anastasia, Thank you for answering! I think you are right and the problem is there, when checking the number of slices in the dwindling file I get: dimensions: 104 x 104 x 72 Although the original dwindling data has: 104 x 104 x 72 x 111 voxel sizes: 2.019231, 2.019231, 2.000000 type: SHORT (4) fov: 210.000 dof: 0 xstart: -105.0, xend: 105.0 ystart: -105.0, yend: 105.0 zstart: -72.0, zend: 72.0 TR: 3670.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9897, y_r = 0.1290, z_r = -0.0618, c_r = -1.2731 : x_a = -0.1108, y_a = -0.9647, z_a = -0.2389, c_a = -22.2682 : x_s = -0.0904, y_s = -0.2296, z_s = 0.9691, c_s = 12.8890 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.9985 0.2605 -0.1236 93.5531 -0.2238 -1.9480 -0.4778 107.8607 -0.1826 -0.4636 1.9382 -23.2834 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 8.15459 ras to voxel transform: -0.4901 -0.0549 -0.0448 50.7312 0.0639 -0.4778 -0.1137 42.9079 -0.0309 -0.1194 0.4845 27.0558 0.0000 0.0000 0.0000 1.0000 I don't understand why, given those are outputs of recon-all .. Do you think you know what's happening? Thank you very much!? Best, Cecilia Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen

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Errors running TRACULA (data attached) - valid frame numbers
by Mazzetti, C. (Cecilia) 06 Oct '19

06 Oct '19

External Email - Use Caution Dear members, I've tried troubleshooting but can't wrap my head around this. Trying to run TRACULA after recon-all the subjects, but I keep getting: ################ [...] R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. (a bunch of these) TR=3670.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.989717, -0.110817, -0.0904434) j_ras = (-0.128995, 0.964706, 0.22957) k_ras = (-0.0618111, -0.238876, 0.969081) keeping frames 0 1 12 23 34 45 56 67 78 89 100 ERROR: valid frame numbers are between 0 and 0 trac-preproc exited with ERRORS ##### I checked the # of bvals and bvecs in the dorm folder compared to orig ones, same. I don't know what's wrong below config file: set subjlist = ( subject02_C ) set dcmlist = ( /myfolder/freesurfer/subject02_C/dmri/data.nii.gz ) set bveclist = ( /myfolder/freesurfer/subject02_C/dmri/bvecs ) set bvallist = ( /myfolder/freesurfer/subject02_C/dmri/bvals ) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 ?set doregmni = 1 set doregcvs = 0 set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) Please any sort of input/help is super appreciated. Let me know if I can give more information Cheers, Cecilia ?

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Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 7
by Juan Rivas 05 Oct '19

05 Oct '19

External Email - Use Caution Thank you for your answer, I pursued your recommendations, and now the warning is that it can open file....../COR-.info. What can I do? JC. El sáb., 5 oct. 2019 a las 12:00, <freesurfer-request(a)nmr.mgh.harvard.edu> escribió: > 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: Curvature estimation from Hessian (LOSKE, PHILIPP (PGR)) > 2. Segmentation faule recon-all (Backhausen, Lea) > 3. Tracula (Juan Rivas) > 4. Re: Tracula (Yendiki, Anastasia) > 5. Question on Z-scoring (Nillo, Ryan Michael R) > 6. ERROR gtmseg (Marina Fern?ndez) > 7. Re: Question on Z-scoring (Greve, Douglas N.,Ph.D.) > 8. Re: ERROR gtmseg (Greve, Douglas N.,Ph.D.) > 9. Re: Segmentation faule recon-all (Greve, Douglas N.,Ph.D.) > 10. Vertex by Vertex Analysis (WON JONG CHWA) > 11. Re: question about aparcstats2table (Kiyotaka Nemoto) > 12. Brodmann area parcellation (sang ho shin) > 13. Errors running TRACULA (data attached) - valid frame numbers > (Mazzetti, C. (Cecilia)) > 14. Confidence interval for Cohen's d from gamma/rstd > (Caspar M. Schwiedrzik) > 15. Re: Errors running TRACULA (data attached) - valid frame > numbers (Yendiki, Anastasia) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 4 Oct 2019 16:27:51 +0000 > From: "LOSKE, PHILIPP (PGR)" <p.loske.18(a)abdn.ac.uk> > Subject: Re: [Freesurfer] Curvature estimation from Hessian > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > AM0PR0402MB36506BB2F6A775BE1ACFC1F9E89E0(a)AM0PR0402MB3650.eurprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hi Bruce, > > thank you for your explanation. I think I might have an idea, why the > Hessian matrix works in this case, maybe you can confirm or correct me if > I'm wrong. Usually, if you're having a 2d surface in space, the principle > curvatures are the eigenvalues of the shape operator (which needs > calculation of first and second fundamental form), not the Hessian. Only in > the particular case of a vanishing gradient, the eigenvalues are the same > as those of the Hessian. F.e. for a quadratic function, the gradient > vanishes at the minimum (in 1d first derivative is zero). Since you're > modelling a quadratic function in a local neighborhood around each vertex, > its minimum lies at the vertex, is that correct? if this is so, then the > gradient should vanish and Hessian matrix should be fine and my confusion > is resolved :). In the literature I found just vague explanations, > sometimes mentioning the shape operator, sometimes the Hessian. I just want > to make sure I understand this process correctly. > > Cheers > Philipp > > > Date: Thu, 3 Oct 2019 10:03:52 -0400 (EDT) > > > Hi Philipp > > the Hessian is estimated at each vertex by doing a quadratic fit to the > local surface as the height function over the tangent plane of all the > vertices in a 2-neighborhood of that vertex. I'm not sure what the gradient > vanishing is about, but the curvatures are just the eigenvalues of the > Hessian, so I don't think the gradient has anything to do with it. Not that > we also have some discrete tools for computing curvature > > make sense? > cheers > Bruce > On Thu, 3 Oct 2019, LOSKE, PHILIPP > (PGR) wrote: > > > > > ????????External Email - Use Caution???????? > > > > Hi, > > > > I am trying to understand how exactly FreeSurfer estimates the curvature > > values from the white surface. From the mailing lists I understood that > the > > white surface is modeled by fitting a second-order polynomial function > and > > curvatures are estimated from the Hessian matrix at each vertex (thank > you > > Bruce). However, I still have trouble to understand how this works in > > detail. First, as I understand it, curvature can only be derived from the > > Hessian if the gradient vanishes (why is this the case?), and from > > differential geometry, shouldn't instead the shape operator be > calculated at > > each vertex on the surface? Second, are the Gaussian and mean curvatures > > then directly calculated from?Hessian/Shape operator or first principle > > curvatures (and are they saved somewhere?). I tried to find a detailed > > explanation in some of the FreeSurfer papers, but couldn't find anything > > really. > > > > Thank you very much in advance! > > > > Cheers > > Philipp > > > > The University of Aberdeen is a charity registered in Scotland, No > SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. > SC013683. >

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Segmentation faule recon-all
by Backhausen, Lea 04 Oct '19

04 Oct '19

External Email - Use Caution Dear FreeSurfer experts, when running the recon -all -all command (I included the -3T flag) with FreeSurfer Version 6.0.0 I get this error for one of my subjects: MRInormalize: could not find any valid peaks. Make sure the Talairach alignment is correct! I added the recon-all log to this email. Is there a way to fix this? Thank you for any suggestion! Best, Lea Backhausen ---------------------------------------- Lea Backhausen PhD Student / Psychologist (M.Sc.) Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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ERROR gtmseg
by Marina Fernández 04 Oct '19

04 Oct '19

External Email - Use Caution Dear experts, The following error occurs with one subject when I am running gtmseg command: *Computing colortable* *ERROR: cannot find match for subcortical segid 229* *ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo* *gtmseg existed with errors* *ans=1* Do you know what happened with this subject? What can I do to solve it? Thank you very much in advance. Marina.

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