Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

Centos 7 - freesurfer hippocampal subfield visualization
by Vetterman, Richard 28 Aug '17

28 Aug '17

Dear freesurfer experts, after an update of my computer I finally use Centos 7 now. It seems as if some parts of the lateral hippocampal subfield segmentation are not visualized any more when using freesurfer. When using FSL, everything looks fine, though. Do you have any suggestions, what to do? Thanks, Richard

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PhD position in collaborative predictive analytics (Munich)
by Dominic Dwyer 28 Aug '17

28 Aug '17

An immediate full-time PhD position is available for an outstanding researcher in the Section for Neurodiagnostic Applications at the Dep. of Psychiatry and Psychotherapy, LMU Munich, directed by Prof. Nikolaos Koutsouleris. The position involves the development of cloud-based predictive applications for an unprecedented Europe-USA international collaborative project called HARMONY (Harmonization of At Risk Multisite Observational Networks for Youth Consortium: Toward the Validation of Biomarkers for Clinical Trials) and for a large-scale Europe-wide project being directed by Prof. Koutsouleris; PRONIA (www.pronia.eu) The main goal is to construct reliable predictive tools that optimally integrate clinical data, neuroimaging, neurocognitive, genetic/metabolic information using state-of-the-art machine learning techniques to predict outcomes of clinical high-risk and first-episode stages of psychosis and depression. The candidate should have experience in MATLAB programming and predictive analytics, machine learning, database management, and model visualization, or some combination of these. These skills are needed to further develop cutting-edge machine-learning techniques being developed at the neurodiagnostics laboratory, including unsupervised and semi-supervised clustering techniques and ensemble learning methods. A profile with evidence of inter-disciplinary flexibility is a positive, evidence of good strategic thinking ability is favourable, and good communication skills are required (fluent English). The minimum degree requirement is M.Sc. (or equivalent) and salary is according the German TV-L E13 scale depending on the academic level of the applicant. The position is initially limited to one year but with the possibility of extension. The position is located at the core of a multi-site international project with a young, dynamic, and multidisciplinary team that is rapidly growing and poised to make significant contributions to the field using unique datasets and cutting-edge methods. Long-standing cooperations also exist with the Section for Biomedical Image Analysis (Christos Davatzikos), the NAPLS 3 coordinating team at Yale University (Ty Cannon), and the Melbourne Neuropsychiatry Centre (Christos Pantelis). Review of applications will begin immediately and will continue until the position is filled. Applicants should send their Curriculum Vitae along with a statement of academic interests and the details of two professional references to: Nikolaos Koutsouleris, nikolaos.koutsouleris(a)med.uni-muenchen.de.

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Recon-all error
by Bronwyn Overs 27 Aug '17

27 Aug '17

Dear mailing list, I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache But for each image the process exits with the following errors: --------------------------------------------------- #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -------------- ----------------------- mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.… <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.…>) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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Error with recon-all long
by Bronwyn Overs 27 Aug '17

27 Aug '17

Dear freesurfer mailing list, I have been running the recon-all -long command and received the following errors: #-------------------------------------------- #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASEID_001/scripts mris_register -curv -nosulc -norot /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg... reading template parameterization from /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.smoothwm): surface doesn't match /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 18:07:29 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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Reliability of labeling procedure in the same scan
by anonymous anonymous 26 Aug '17

26 Aug '17

Hi all, Without noticing I run recon-all twice on the same scan of the same subject and we noticed there are some differences, at least in the hippocampal volume estimation. Is it normal? If it is, why is it so? Thank you so much for your help This is a great community!

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Labels from Pial surface
by Fereshte 26 Aug '17

26 Aug '17

Hello FreeSurfer developers, Is it possible to have the segmentation labels after the pial surface is done in FreeSurfer? I mean once you do the topology correction and expand the inner cortical boundary to make the pial surface ; is it possible to have the inner and outer cortical boundaries as labels from pial surface? Looking forward to hearing from you Sincerely, Fereshte Ramezani

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Change the template in Freesurfer
by YQ Chen 26 Aug '17

26 Aug '17

Hi, I want to change the template when doing recon-all. Is it possible? If it can, how can I do? Tell me, please! Thanks a lot! YQ

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dividing cortex into equal patches
by Aniqa Dalowr 26 Aug '17

26 Aug '17

Hi All, I want to divide the cortex into patches that have the ~ same surface area. Is there a quick way to do that ? Please let me know, Thanks Ani

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Re: [Freesurfer] Pial surface editing
by Michelle VanTieghem 25 Aug '17

25 Aug '17

Hi, Yes, I am trying to use skull stripping from another package, since -gcut option did not work on our data for appropriate skull stripping, and as a result there is too much pial matter included as white matter. a) Is brainmask.mgz an appropriate input file for recon-all -all? for example, should I run "recon-all -all -i brainmask.mgz -s SB001" ? or, am I still using the original .dcm file as input, and merely putting a copy of my skull stripped brain into the SUB/mri directory that was created in the previous processing attempt? b) I am not understanding why i will still run skull stripping in the script here, if it is already done. Is the brainmask.auto.mgz generated just another duplicate copy that will be ignored for the actual segmentations? Will this still perform intensity normalization and other auto-recon1 steps normally? Thank you, Michelle On Tue, Jul 18, 2017 at 12:44 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Michelle > > can you cc the list so others can answers? I'm also no longer sure which > thread this is - were you trying to use the skull stripping from another > package? If so, convert that file to be named brainmask.mgz, then do *not* > include the -noskullstrip in your command line. Let us do the skull > strippping, which will create a brainmask.auto.mgz, but should preserve the > brainmask.mgz (since it is different than the .auto file) > > cheers > Bruce > > > > On Tue, 18 Jul 2017, Michelle VanTieghem wrote: > > >> Hi Bruce, >> >> >> Thanks for the information. Sorry I had changed my mail settings so I >> wasn’t >> seeing your responses until now. I had tried to run all, but just >> skip skull >> strip step, as well as the talaraich check step since we saw errors with >> that too. >> >> The command I used is follows: >> >> recon-all -all -3T -mprage -notal-check -noskullstrip >> -i/vega/psych/users/mrv2115/fsdata/ORIG_AFNI_SKULLSTRIP/SB00 >> 1/mprage_deobliqu >> e_brain.nii -s SB001 >> >> However, I am getting the following error during the registration step >> (see >> below). It looks like the mask volume brainmask.mgz hasn't been generated, >> but i don't know why. You suggested to convert my afni skull stripped >> brain >> to brain mask.mgz and place in the MRI folder. but am I still going to run >> the steps of autorecon-1 ? (intensity normalization, etc)? Does recon-all >> take inputs of already existing mri/brainmask.mgz files? It seems like it >> just needs one file and then re-generates a new directory with mri, >> scripts, >> ect. I would appreciate more detail on how to implement this! >> >> Thank you, >> >> Michelle >> >> >> ERROR: >> >> >> >> ======= NUMBER OF OPENMP THREADS = 1 ======= >> >> aligning to atlas containing skull, setting unknown_nbr_spacing = 3 >> >> using MR volume brainmask.mgz to mask input volume... >> >> reading 1 input volumes... >> >> logging results to talairach.log >> >> reading '/vega/psych/app/freesurfer/average/RB_all_2008-03-26.gca'... >> >> average std = 6.9 using min determinant for regularization = 4.7 >> >> 0 singular and 1812 ill-conditioned covariance matrices regularized >> >> reading 'nu.mgz'... >> >> mghRead(/vega/psych/users/mrv2115/fsdata/processed/SB001/ >> mri/brainmask.mgz, >> -1): could not $ >> >> mri_em_register: could not open mask volume brainmask.mgz. >> >> >> Linux bogota.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 >> 00:53:17 EST 2017 x86_$ >> >> >> recon-all -s SB001 exited with ERRORS at Tue Jul 18 11:50:24 EDT 2017 >> >> >> —— >> >> >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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cudadetect fails: wrong amount of memory and number of cores detected
by Markus.Mertens＠evkb.de 25 Aug '17

25 Aug '17

Hello FreeSurfer Developers, I would like to use recon-all with the option "-use-gpu" so I ran cudadetect first to see whether the nvidia card on my system will be detected. But at least the values for total amount of memory and number of cores are wrong (should be 8GB and 2304 cores). $ cudadetect Detecting CUDA... There are 0 devices supporting CUDA: Device 0: "Quadro K5200" CUDA Driver Version: 8.0 CUDA Runtime Version: 6.50 CUDA Capability Major revision number: 3 CUDA Capability Minor revision number: 5 Total amount of global memory: 4224450560 bytes Number of multiprocessors: 12 Number of cores: -2109039396 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 65536 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 2147483647 x 65535 x 65535 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 0.77 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) $ What could I try? Thank you. FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz uname -a: Linux cortex 4.4.74-server-1.mga5 #1 SMP Mon Jun 26 08:34:35 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux _______________________________________________________________ Evangelisches Klinikum Bethel gGmbH Akademisches Lehrkrankenhaus der Universität Münster Sitz der Gesellschaft Kantensiek 11 | 33617 Bielefeld Amtsgericht Bielefeld HRB 30169 Geschäftsführer Dr. Rainer Norden (Vorsitz) Dr. Matthias Ernst Dr. Maren Thäter Vorsitzender des Aufsichtsrates Pastor Ulrich Pohl 150 Jahre Bethel - Für Menschen da sein

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Freesurfer August 2017