Freesurfer

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Freesurfer Problem Report
by Timothy Hendrickson 11 Dec '15

11 Dec '15

Freesurfer experts and/or developers, I ran a recon-all on a particular subject. When I attempted to open the subject in freeview I received an error, which is below. Here is the information requested when submitting a freesurfer problem report: FREESURFER_HOME: /opt/local/freesurfer-5.3/x86_64 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.7 (Santiago) Kernel info: Linux 2.6.32-504.1.3.el6.x86_64 x86_64 1) subject name: *47266_SE003* 2) the entire command-line executed: *manualEdits 47266_SE003* (included the script manualEdits.sh as an attachment) 3) the error message generated: *freeview.bin: ../../src/mesa/tnl/t_vertex.c:423: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed.Abort (core dumped)* 4) optionally include the subject's /script/recon-all.log Please let me know if you require additional information. -Tim -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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questions about summary of Monte Carlo simulation‏
by Karl Liu 11 Dec '15

11 Dec '15

Dear Freesurfer experts, I repost my question from yesterday since it is not answered. Thanks in advance for any help. After running Monte Carlo simulation from the command line, I noticed two cluster summary files are produced for each contrast: cache.th20.neg.sig.cluster.summary and mc-z.neg.th20.sig.cluster.summary. They are quite similar, with different number of surviving clusters in some cases. I am wondering which is the one to report final results. Will you explain a bit more about the differences between them? Also, after reading the summary file, we still have to visualize the results. If the MC simulation is done in QDEC GUI, then the QDEC automatically presents the outcome from mc-z.neg.th20.sig.cluster.mgh, but I am not sure if this is the right file. I am using FS version 5.3 without tksurferfv. I found the tksurfer is running quite slow and unresponsive. Any other suggestions? Thank you very much! Karl

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R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 11 Dec '15

11 Dec '15

Thanks, in which folder I should put this file? Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 7-dic-2015 19.23 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] FDR in FS-FAST > > > >On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >> Hi list, >> I have two concerns, please: >> 1) It is possible to apply FDR correction on rs-fMRI seed based >> analysis by FS-FAST? If yes, I can I do it? >try this binary >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr >> 2) I have apply the FS guidelines and I have used Montecarlo >> correction with threshold at 1.3 but in the within group analysis the >> clusters are very large. In the guide I read examples with a threshold >> at 3. Is there a specific reason? >There is not a hard-and-fast criteria for the voxel-wise threshold. 3 is >fine as is 1.3 >> Thanks >> >> Stefano >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >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. > >

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average cortical thickness measure?
by Maria Kharitonova 11 Dec '15

11 Dec '15

I know that the aseg atlas provides a number of voume measures (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a variable for an average cortical thickness? I'd like to see if thickness in some of the regions is associated with a variable of interest over and above an overall main effect, so would like to control for the average thickness, but can't figure out a good way to do that. Thanks! Maria - Maria Kharitonova, PhD Research Assistant Professor Department of Medical Social Sciences Northwestern University Feinberg School of Medicine 625 N. Michigan Ave, Suite 2700 Chicago, IL 60611 Phone: (312) 503-6503 Email: maria.kharitonova(a)northwestern.edu<mailto:maria.kharitonova@northwestern.edu>

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Freeview PETSC Error
by Udunna Anazodo 11 Dec '15

11 Dec '15

Hi, I downloaded and installed Freesurfer stable release 5.3 distribution linux_centos4_x86_64 on an Ubuntu 12.04 system. However freeview crashes with a PETSC error. I read the freesurfer archives and followed the instructions found on https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-November/041243.…. I downloaded the most recent version of freeview.bin using wget as suggested but I still get the same error message. Any ideas how to work around this. Thanks [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 udunna-work by udunna Thu Dec 10 17:42:30 2015 [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 -- Udunna

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Convert TAL coordinates to surface RAS coordinates
by Inês Violante 11 Dec '15

11 Dec '15

Dear experts, I have a set of Talairach coordinates that I want to convert to the individual subject surf RAS coordinates. How can I do this? Thank you very much. Ines

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Question about running recon-all with deface
by Mishra, Virendra 10 Dec '15

10 Dec '15

Hello, We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject's recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face . To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help) 1) Step 1: mri_deface -i original_T1 -o deface_T1 2) Step 2: recon-all -i deface_T1 3) Step 3: recon-all -i original_T1 -deface 4) Step 4: recon-all -i original_T1 5) The results from Step 3 is exactly equal to Step 4 6) The results from Step 2 and Step3/4 have errors >20% in certain regions. 7) Step 1-4 are done with version 5.3.0 Any response will be greatly appreciated. Thanks Regards Virendra =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Shifted surface after gyrification index is calculated
by Chris Holdgraf 10 Dec '15

10 Dec '15

Hey Freesurfer folks - I'm looking into using Freesurfer for doing electrode reconstruction / co-registration in electrocorticography. We're making good progress on figuring out recon-all for surfaces and doing co-registration to CTs. However, I think I've encountered a strange bug. I'm trying to create a smoothed pial surface so that I project electrodes onto this surface. The code seems to run correctly, however, the smoothed surface looks translated relative to the original pial surface that it was created from. For example, see this issue I opened on github: https://github.com/aestrivex/gselu/issues/7 Anyone have an idea why this is happening? I'm not sure why the pial surface would be correct, while the smoothed surface would be shifted. Chris -- _____________________________________ PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/> Editor and Web Director | Berkeley Science Review <http://sciencereview.berkeley.edu/> _____________________________________

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reg-feat2anat error ("mri_convert ERROR: could not determine file")
by Emily Coffey 10 Dec '15

10 Dec '15

Hello, I am having a similar problem to that posted several times previously. I get an error when running reg-feat2anat to register FSL feat files to the freesurfer reconstruction, see: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038437.html because the subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii file does not seem to make itself. I'm wondering where I can find an active link to an updated reg-feat2anat, as all the links I find in threads are not working. I did find a potential workaround: if I create the /mri/tmp directory and convert the .mgz file from the freesurfer output to .nii here, as explained on this website (http://wikis.la.utexas.edu/imagelab/book/how-convert-mgz-structural-files-n…) I can create the missing nii file and rerun the registration, however, I'm uncertain about the orientation parameters as although the orientation of the nii matches that of my original T1, the resulting registration in freesurer is nonsense. Example of the command I am using to manually convert the .mgz to nii: mri_convert --in_type mgz --out_type nii subjectsfreesurferfolder/mri/brainmask.mgz --out_orientation RAS subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii Any suggestions on either the updated file location or the workaround much appreciated! Notes: I am running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 On Linux: Ubuntu 12.04.5 LTS Emily

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Freesurfer 6 exits with errors after recon edits on skullstrip
by Tuominen, Lauri Johannes 10 Dec '15

10 Dec '15

Dear Freesurfer experts, I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but part of the occipital cortex was missing and I therefore ran the following command ( both in freesurfer6 ): recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib This took care of the brain mask problem that I had with the previous recon. So I then ran on launchpad: recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1' The last command exits with errors. Please find the log-files attached. Thank you for your help! Best, Lauri Tuominen

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