Freesurfer

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30083 discussions

bug in freesurfer-dev (T2-specific parameters not passed to second call of mri_make_surfaces)
by Marco Aqil 28 Aug '19

28 Aug '19

External Email - Use Caution Hi, I would like to report a bug in freesurfer-dev. I have encountered this bug in a version downloaded on July 11th, 2019, and again in a version downloaded two days ago (August 20th). In short, it seems that parameters specified via an expert file relevant to T2-assisted pial segmentation, such as -T2_min, are not passed to the second call of mris_make_surfaces (the one actually using T2 data). In Freesurfer 6.0.0, this is not the case, and the T2_min parameter is indeed passed to the second call of mris_make_surfaces (although I note that in 6.0.0, when specifying -nsigma_below via the expert file, both the user-specified value and the standard value are passed to the second call of mris_make_surfaces). See below for more details on the specific freesurfer-dev behavior. Best, Marco Aqil Bug description: T2-specific parameters not passed to second call of mri_make_surfaces in freesurfer-dev Call: recon-all autorecon3? -subjid <subject id> -hires -T2pial -parallel -openmp 15 -expert <expert file path> Expert file content: mris_make_surfaces -T2_min 35 >From the recon-all log, the first call of mris_make_surfaces receives the -T2_min parameter: ---------------- #@# Make Pial Surf lh Mon Aug 19 13:43:02 CEST 2019 <scripts folder path> mris_make_surfaces -save-res -save-target -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs -T2_min 35 sub-006 lh ---------------- However, the second call of mris_make_surfaces, which relies on T2 data to refine the pial, does not receive the T2_min parameter, and looks as follows: --------------- #@# Refine Pial Surfs w/ T2/FLAIR Mon Aug 19 14:02:23 CEST 2019 <other T2 pial steps> mris_make_surfaces -save-res -save-target -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-006 lh --------------- I observed the same behavior when specifying -nsigma_below via the expert file.

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Contrast of interaction between covariates in FSGD
by Zhi Li 28 Aug '19

28 Aug '19

External Email - Use Caution Dear Freesurfer experts, May I ask how to understand the contrast of interaction between covariates in the example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V? The interaction of group x age x weight is: [0 0 1 -1 0 0 0 0 0 0 1 -1] Why the interaction between group and weight should be put in the second row (what does each row mean in the F-contrast matrix)? If there are three levels in the factor one (three groups), I guess the interaction of group x age x weight should be: [0 0 0 1 -1 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 1 -1] Is this correct? If not how should I set this contrast? In addition, if I would like to know the interaction between age and weight without group, how should I set the contrast then? Looking forward to your kind suggestions. Thanks and best wishes, Lizhi

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freeview crash -- petsc error when opening volume
by TRISTAN J PAUTSCH 27 Aug '19

27 Aug '19

External Email - Use Caution Greetings all, I'll try to keep this succinct. I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I used the stable 6.0/CentOS 6 download, in addition to the dev version of freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview launches fine and stays open when launched alone, however attempting to open a volume (either through the GUI or directly via the CLI) causes a crash and the following error about 5-8 seconds after launching (brain images begin to populate, then crash): --- [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [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 xxxxxxx by xxxxxxx Tue Aug 20 13:44:15 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 Segmentation fault (core dumped) --- I've seen a number of other posts on the mailing list about this, but all of them I could find either end abruptly without a solution or with an unanswered request for more info. Happy to provide any additional information or anything that may aid in the resolution of this issue. Thanks everyone, ~T

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Post-doctoral Fellowship in Human Perceptual Neuroscience at New York University
by Max Levinson 27 Aug '19

27 Aug '19

External Email - Use Caution The Perception and Brain Dynamics Laboratory (PI: Biyu J. He, Ph.D., http://www.med.nyu.edu/helab/) at New York University is currently recruiting for a post-doctoral fellow to conduct research to illuminate how prior knowledge shapes perception in the human brain. The position is funded by National Science Foundation (NSF) and is renewable yearly for up to 4 years. The planned research project involves a combination of cutting-edge human brain imaging technologies, including ultra-highfield (7 Tesla) fMRI and magnetoencephalography (MEG) in healthy subjects, electrocorticography (ECoG) in neurosurgical patients, along with psychophysics and neuropsychology. We are looking for a candidate with a passion for perceptual and cognitive neuroscience, independent critical thinking, strong analytical and quantitative skills, and good interpersonal skills. Experience with human brain imaging (such as fMRI, MEG, or ECoG) and excellent programming skills are highly desirable. Our laboratory is located on the medical campus of New York University in Manhattan, NY, and is affiliated with the Neuroscience Institute, Department of Neurology, and Department of Radiology. The position is expected to start in fall-winter of 2019, but early spring of 2020 is also possible. We provide competitive salary and benefits that adjust for cost of living in New York City. To apply, please send a CV, a cover letter, a statement of scientific and career goals, and names and contacts of three referees to Prof. Biyu Jade He (email: biyu.jade.he(a)gmail.com) with the subject line “post doctoral application 2019”. We strongly encourage interested candidates to apply as soon as possible, but no later than Oct 15.

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binary version of brainmask?
by Chris Adamson 26 Aug '19

26 Aug '19

External Email - Use Caution Freesurfer, Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz? Thank you, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Invalid License Key Error for Freesurfer 5.1
by An Lijun 26 Aug '19

26 Aug '19

External Email - Use Caution Hello Freesurfer developers, Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0 version and it seems not applicable for 5.1.0 since I still got the same error message as before. May I ask how to get the licnese of 5.1.0? Thanks for your help! ----------------------------------------------------------------------------------------------------------------------------------- Best Regards, An Lijun

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trouble with freeview View > Show Color Scale
by Elizabeth Olson 26 Aug '19

26 Aug '19

External Email - Use Caution Hello, I'm having a bit of trouble with the Show Color Scale option. I have run TRACULA and have loaded a text file containing p-values from an analysis (Spline Color: Heatscale, Scalar map: my p-values file). The values display correctly on the tract. However, when I use View > Show Color Scale, it looks like the color scale is generated is for the black-and-white volume, instead of for those values. See attached screenshot. I'm instead trying to generate a Color Scale at the right of the figure that shows which colors (yellow to red) correspond to which p-values. Thanks for your help, Liz

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Re: [Freesurfer] mri_vol2surf fails
by Greve, Douglas N.,Ph.D. 26 Aug '19

26 Aug '19

Are those values actually 0 or just very small? Is that area dark on the T2*? On 8/26/19 11:20 AM, Sackl, Maximilian wrote: > External Email - Use Caution > > Thank you for the prompt answer! > > No, the T2* map within the pial and WM does include values ... > Any ideas? > > On 26.08.2019 16:59, Greve, Douglas N.,Ph.D. wrote: >> You should bring up the T2* with the surfaces. Is it possible that the >> T2* just did not include that particular bit? >> >> On 8/26/19 10:38 AM, Sackl, Maximilian wrote: >>> External Email - Use Caution >>> >>> Dear FreeSurfer experts, >>> >>> I was trying to perform a GLM fit with T2* data, projected on the >>> cortical surface. >>> >>> For the preparation of the 4D-input file (needed for mri_preproc) I used >>> the mri_vol2surf command and encountered the following problem. There >>> appear regions without any values, (screenshot mri_vol2surf_output.png), >>> although the segmentation of the pial and WM surface seem to be correct. >>> (screenshot pialSurface.png). >>> >>> Do you have any idea, how to solve this problem? >>> >>> >>> Thank you very much! >>> >>> Best regards, >>> Maximilian >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Question re: hippocampal & amygdala subdivision files.
by Jamie Hanson 26 Aug '19

26 Aug '19

External Email - Use Caution Dear Freesurfer List, I had a (hopefully) quick question re: output files from the hippocampal and amygdala subdivision routines. I know that there are multiple parcel schemes for the hippocampus (HBT, FS60, and CA), and per this thread ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57898.html) the final subfield segments are "computed from none of those volumes, but the parent of all of them". I wondered however if there was an MGZ file that corresponded to the final/combined sub-divisions? Or if there was a way to output this? My group was interested in doing some spatial and surface analyses of sub-divisions (using Spherical Harmonics or some other related techniques). And I understand what the different MGZ files were in the mri directory (e.g., CA.FSvoxelSpace.mgz, FS60.FSvoxelSpace.mgz, HBT.FSvoxelSpace.mgz), but what was the file without any suffix (e.g., lh.hippoAmygLabels-T1.long.v21.mgz)? Or is that the file I'm looking for? Any information is deeply appreciated! Thanks much, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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mri_vol2surf fails
by Sackl, Maximilian 26 Aug '19

26 Aug '19

External Email - Use Caution Dear FreeSurfer experts, I was trying to perform a GLM fit with T2* data, projected on the cortical surface. For the preparation of the 4D-input file (needed for mri_preproc) I used the mri_vol2surf command and encountered the following problem. There appear regions without any values, (screenshot mri_vol2surf_output.png), although the segmentation of the pial and WM surface seem to be correct. (screenshot pialSurface.png). Do you have any idea, how to solve this problem? Thank you very much! Best regards, Maximilian -- Maximilian Sackl, BSc Department of Neurology Medical University of Graz Auenbruggerplatz 22, A-8036 Graz maximilian.sackl(a)medunigraz.at www.neuroimaging.at Tel +43/316/385-13691

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