Freesurfer October 2019

freesurfer@nmr.mgh.harvard.edu

111 participants
180 discussions

Corpus Callosum area
by Fernanda Hansen P. de Moraes 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer experts, how can I extract the corpus callosum cross sectional area for each hemisphere? Thank you very much in advance, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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mri_surf2vol -lost cluster
by Albrecht, Daniel S. 07 Oct '19

07 Oct '19

Hello everyone, I've been using mri_vol2surf to move some activation data in MNI space to the fsaverage surface with the following command: mri_vol2surf --mov MNIvol.nii --projfrac-max 0 1 0.1 --hemi rh --o rh.out.mgz --mni152reg This works well, but I'm losing a small temporal gyrus cluster that sits close to pial surface. I was assuming this was due to the proximity to the pial surface and resampling, but are there any other options or flags I could use to get this to project successfully? Thanks very much, Dan

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What's the difference between FSFAST and SPM in the 1-st level GLM?
by Zhi Li 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer experts, May I ask what's the difference between FSFAST and SPM in the 1st level GLM? Now I use fsfast to pre-process my task-based imaging data, then model the data with FSFAST and SPM respectively. I expected to get very similar results from FSFAST and SPM in the whole brain volume-based analysis. Although there is some overlap between FSFAST and SPM on the whole brain activation, however, there is a lot of difference. Activation in some regions based on SPM was not found in that based on FSFAST. Please see below for my mkanalysis information: mkanalysis-sess \ -fsd Num -mni305 2 -fwhm 8 \ -event-related -paradigm Num.par -nconditions 18 \ -spmhrf 0 -TR 2 -refeventdur 16 -nskip 0 -polyfit 0 \ -hpf 128 -mcextreg \ -analysis Num.sm08.mni305 -per-run -force Any suggestions? In addition, I am not clear if I convert the volume data from FSFAST to SPM in a right way. I replace the mask of subcortical mask with the whole brain mask. Then I convert the pre-processed data from mni305 to mni152 and model it with SPM. However, there is a lot of loss in the prefrontal and subcortical regions. Seems like the whole brain data shrinkage in SPM (please see attached figure). Looking forward to your kind reply. Thanks and best, Li Zhi

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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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Freesurfer October 2019