Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30097 discussions

Re: [Freesurfer] Bug in Freesurfer Installation
by Aman Montazeri 15 Jul '16

15 Jul '16

Im not sure if its the problem or not, but seems that its the file permission error. Either do "sudo su" and re-run your command as root or change the file permissions in /subjects folder. Running commands as "root" is generally not recommended. On Jul 15, 2016 4:41 PM, "Sherryse Corrow" <sherryse.corrow(a)icloud.com> wrote: Hello freesurfer developers, I installed FreeSurfer on my computer today using the instructions found here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. After installation, I proceed to the “test your FreeSurfer Installation” section. Upon trying the first test, I ran the following and code and received the following error. Sherryses-iMac:~ sherrysecorrow$ cd $FREESURFER_HOME/subjects Sherryses-iMac:subjects sherrysecorrow$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... niiWrite(): error opening file sample-001.nii.gz ERROR: failure writing sample-001.nii.gz I’ve searched the list and was unable to find someone with the same error in the archives. Any thoughts on how to fix this? freesurfer-Darwin-lion-stable-pub-v5.3.0 Mac OS X version 10.9.5 uname -a Darwin Sherryses-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 Thanks, Sherryse _______________________________________________ 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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Re: [Freesurfer] XQuartz 2.7.9 update results in errors
by Robert C Welsh 15 Jul '16

15 Jul '16

Hi Zeke, I’m seeing the same issue (running xquartz 2.7.9 on MacBooPro10,1). XQuartz 2.7.8 works, 2.7.9 breaks both freeview, tkmedit, qdec I’ve also submitted bug report to xquartz, https://bugs.freedesktop.org/show_bug.cgi?id=96849 <https://bugs.freedesktop.org/show_bug.cgi?id=96849> The errors thrown are: rcwelsh@mnemosyne:/home/Software/fs_install/bin$ qdec X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1184 Current serial number in output stream: 1185 rcwelsh@mnemosyne:/home/Software/fs_install/bin$ tkmedit X Error of failed request: GLXBadContext Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 6 (X_GLXIsDirect) Serial number of failed request: 26 Current serial number in output stream: 25 rcwelsh@mnemosyne:/home/Software/fs_install/bin$ freeview X Error: BadValue (integer parameter out of range for operation) 2 Extension: 150 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x18001d8 [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 mnemosyne by rcwelsh Thu Jul 7 14:56:12 2016 [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 X Error: GLXBadContextTag 164 Extension: 150 (Uknown extension) Minor opcode: 1 (Unknown request) Resource id: 0x960005 -Robert ------------------------------------------------------------------------------------------------------------------------------------------------------ Hello Kate, Thanks for the information. We have seen similar behavior with previous XQuartz releases in the past as well. This tends to "freeze" certain vesion of OSX with certain versions of XQuartz. I will take a closer look but this is usually something that we have to deal with. -Zeke On 06/20/2016 08:34 PM, Kate Mills wrote: > Hi All, > > My lab is having difficulty loading the freeview gui after updating to > the latest version of XQuartz (2.7.9). We were wondering if others have > experienced this issue? We have reverted by to XQuartz 2.7.8 on our > machines for now. In case relevant, this errors seems to span Mac OS > versions. > > Thank you! > > Kate > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> ---------------------------------------- Robert C. Welsh, Ph.D. Associate Professor Department of Radiology Department of Psychiatry University of Michigan rcwelsh(a)umich.edu Associate Director, VA-fMRI Research, VA Ann Arbor

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Obtaining White and pial surface maps for multiple subjects
by Dev vasu 15 Jul '16

15 Jul '16

Dear sir, I would like to know how could i possibly generate white and pial surface data for pool of 50 subjects ( 25 healthy controls and 2 subjects with BLVP) using free surfer. Thanks Vasudev

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Re: [Freesurfer] RB_all_2008-03-26.gca
by Gabor Perlaki 15 Jul '16

15 Jul '16

Dear Bruce, Some subcortical structures seems to be suboptimally segmented in our subjects. By looking at the original MRI intesities and labels of the atlas subjects individually we may suspect that the segmentation of these structures were also suboptimal in the atlas subjects (so the gca atlas is suboptimal), or it is rather related to some demographic/disease related differences between the training data and our subjects, and/or it is a segmentation algorithm related issue. Best Regards, Gabor 2016-07-14 15:30 GMT+02:00 Gabor Perlaki <petzinger.gabor(a)gmail.com>: > Dear all, > > Is it possible somehow to visually inspect the segmentations of the > individual subjects used for the RB_all_2008-03-26.gca atlas? I can extract > the means, priors and labels, but I am rather interested in the original > MRI intensities and labels for the individual subjects. > > Best Regards, > Gabor > > <petzinger.gabor(a)gmail.com> > -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor(a)gmail.com

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Freesurfer autorecon2 problem
by Li,Tengfei 15 Jul '16

15 Jul '16

Dear Freesurfers, I am now trying to do recon-all -autorecon1 and recon-all autorecon2 and then do the quality control. When I try " recon-all -autorecon1 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " It works. However, next when I do " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 " or " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " I always get an error. and the error message is " recon-all -s ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 exited with ERRORS at Thu Jul 14 18:19:02 CDT 2016 For more details, see the log file /workspace/tli3/freesurfer_try_onestep_0559_0815/ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582/scripts/recon-all.log " Could someone help me with this? Thx! Best Tengfei The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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freesurfer autorecon2 problem
by Li,Tengfei 15 Jul '16

15 Jul '16

Dear Freesurfers, I am now trying to do recon-all -autorecon1 and recon-all autorecon2 and then do the quality control. When I try " recon-all -autorecon1 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " It works. However, next when I do " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 " or " recon-all -autorecon2 -subjid ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 -notal-check " I always get an error. and the error message is " recon-all -s ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582 exited with ERRORS at Thu Jul 14 18:19:02 CDT 2016 For more details, see the log file /workspace/tli3/freesurfer_try_onestep_0559_0815/ADNI_002_S_0559_MR_MPRAGE_br_raw_20080821223915203_1_S55646_I116582/scripts/recon-all.log " Error report is attached. Could someone help me with this? Thx! Best Tengfei The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Research Position
by Mcnorgan, Christopher 14 Jul '16

14 Jul '16

Hi Freesurfers, I wanted to bring to the attention of recent graduates a research assistant position in my lab. Briefly, the position entails the application and transfer of your proficiency with FreeSurfer in the acquisition and analysis of fMRI data collected from healthy adults. More details can be found at the URL below: https://www.ubjobs.buffalo.edu/applicants/jsp/shared/position/JobDetails_cs… Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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question about stats
by Zachariah Holub 14 Jul '16

14 Jul '16

I have run various batches of freesurfer on our MRI scans. Now I want to take many of the stats files from all of our subjects and export them to one giant excel document. I would like to have a separate sheet for each kind of statistic (i.e. Sheet1=LH aparc.2009a; Sheet2=RH aparc.2009a; Sheet3=LH DKT etc...) and then have all of the subjects for that statistic type be included in the appropriate, single sheet. Is there a program that you are aware of that I can use to export the stat files to excel? I would greatly appreciate any insight or help you can offer as it is taking me forever to do this by simply copy and paste. Thank you in advance,Zach

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command line for cp in freeview
by Mihaela Stefan 14 Jul '16

14 Jul '16

Hello Freesurfers, What is the command line to load the control.dat file (control points) in freeview? We tried -cp but it didn't work. Thanks! Mihaela

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mpr2mni305 failed
by Marita Partanen 14 Jul '16

14 Jul '16

Hi I have run recon-all successfully in the past, but now I am getting an error of mpr2mni305 failed, see transforms/talairach_avi.log. I'm running freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac 10.10.5. This issue appears the same as a recent post http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47393.html but I couldn't see a solution. Any ideas? Here's the full error log: /Users/ophthalmologylab/Studies/Dyslexia_MRI/Intervention/freesurfer/DEGDY001B/mri /Applications/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Darwin cfri2163m.bcricwh.lan 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 Fri Jun 17 13:29:22 PDT 2016 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.14, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.91038e-11, -3.72529e-09) j_ras = (-3.72529e-09, -5.82077e-11, -1) k_ras = (7.27596e-12, 1, -5.82077e-11) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 126.275; 0.000 -0.000 1.000 -112.522; -0.000 -1.000 -0.000 132.333; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 17 13:29:25 PDT 2016 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 17 13:29:25 2016 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted _________________________________ Marita Partanen, M.Sc., M.Ed. Ph.D. Candidate in School Psychology The University of British Columbia 2125 Main Mall Vancouver, BC V6T 1Z4 partanen(a)alumni.ubc.ca<mailto:partanen@alumni.ubc.ca>

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