Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 149, Issue 31
by Tamara Tavares 18 Jul '16

18 Jul '16

Hi Bruce, Thank you for your quick reply. We are primarily interested in ventricular volume but we may look at other areas in the future; this is why I thought it would be a good idea to check the surfaces. Is the reasoning why the surface outputs vs. aseg outputs should be checked is because the surface outputs are used the calculate the structure's volumes? I am fairly new to Freesurfer so I am trying to get a good understanding of it. Thank you in advance, Tamara --- Tamara Tavares, HBSc <http://H.B.Sc> PhD Candidate Brain and Mind Institute, Department of Neuroscience The Schulich School of Medicine and Dentistry The University of Western Ontario 519-661-2111, ext 84623 On Sun, Jul 17, 2016 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Checking Surfaces vs. aseg outputs (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 16 Jul 2016 13:35:10 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Checking Surfaces vs. aseg outputs > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1607161334500.21946(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Tamara > > if you are more interested in things like ventricular volume then the > surfaces aren't so important to check. > > cheers > Bruce > > > On Fri, 15 Jul 2016, Tamara Tavares wrote: > > > Hi All, > > > > I was hoping to get some help with understanding the surface and aseg > > volumes. I have some patient's scans and I am interested in examining the > > ventricular volume but may look at other areas later on. I understand > from > > earlier threads that it is important to check the surface volumes (pial > and > > wm) vs. the aseg output. Why is it more important to check the surfaces > vs > > the aseg outputs if I am interested in getting the volumes? > > > > Thank you in advance for your help. > > > > Best, > > Tamara > > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 149, Issue 31 > ******************************************* > > > 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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Integrate SPM activation maps to FreeSurfer structural volumes
by Mahtab Farahbakhsh 18 Jul '16

18 Jul '16

Dear FreeSurfer, I am trying to register my SPM activation maps to the structural data of each subjects. Except for the commands I could find for the registration, I could not find a guide on the registration of activation maps from SPM to FreeSurfer. Would you please guide me how I should do that? Best Regards, Mahtab.

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LME contrasts
by Clara Kühn 18 Jul '16

18 Jul '16

Dear FreeSurfer experts, I am following the mass-univariate (spatiotemporal) model in the LME tutorial. My design matrix X has the following columns: intercept, time, time², group1, group1*time, group1*time², group2, group2*time, group2*time², sex, age, mean_thickness I actually have 3 groups but group1 and group2 in X are dummy coded. I would like to check whether there are group differences in the quadratic term but I don't understand what this command expresses and how the contrast was formed: CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)]; Could you please explain it on the example design matrix so I can adapt it to mine? Thank you! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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can not find module 'dev'
by Yun Wang 17 Jul '16

17 Jul '16

Dear All, I recently tried to gain access the read-only CVS source-code repository, however, I have this kind of error: cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules anyone have idea what is going on here? Thank you so much! Best, Yun Wang

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Checking Surfaces vs. aseg outputs
by Tamara Tavares 16 Jul '16

16 Jul '16

Hi All, I was hoping to get some help with understanding the surface and aseg volumes. I have some patient's scans and I am interested in examining the ventricular volume but may look at other areas later on. I understand from earlier threads that it is important to check the surface volumes (pial and wm) vs. the aseg output. Why is it more important to check the surfaces vs the aseg outputs if I am interested in getting the volumes? Thank you in advance for your help. Best, Tamara

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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 July 2016