Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Cortical gray matter volume
by derin＠conte.wustl.edu 12 Jul '06

12 Jul '06

Hi, I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance. -Derin

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stripping MP-RAGEs from Allegra
by Russell Poldrack 10 Jul '06

10 Jul '06

hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping (primarily on the dorsal posterior surface of the skull). I have tried the recommendations from the wiki (reducing the wsthresh to 5, and using -wsatlas) to no avail, there is still skull left over. Short of editing out the scalp by hand, are there any other tricks I might try to get the automated stripping to work? for what it's worth, we have found these Allegra MP-RAGE images to wreak havoc on BSE and BET as well. Any suggestions would be most appreciated! cheers russ --- Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: poldrack(a)ucla.edu web: www.poldracklab.org

2 3

mri_normalize
by Don Hagler 10 Jul '06

10 Jul '06

I am getting an error running mri_normalize (as part of recon-all) on a particular subject's volume. Here is the command from recon-all: mri_normalize -g 1 nu.mgz T1.mgz Here is the output: WM removal version using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.860 -0.007 -0.123 -96.500; -0.087 0.643 -0.647 -17.669; 0.096 0.653 0.636 -156.251; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed nu.mgz looks fine, so I wonder what could be the problem. Any ideas?

2 1

details on subcortical segmentation
by Sasha Wolosin 10 Jul '06

10 Jul '06

Dear all, I am interested in learning more about the details of subcortical segmentation, in particular how the basal ganglia structure boundaries are determined. Is there any literature I may refer to? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 3

old_freesurfer question
by Stefano Pellegrini 10 Jul '06

10 Jul '06

Hi everybody, I have a small problem with an old version of freesurfer. I am studing some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each hemisphere, but I have found only the thickness af each single area of the segmented cortex in a txt file in the label directory. Can anybody please tell me where I can find the information about the average cortical thickness of each hemisphere? Should I recalculate it averaging all the cortical labeled areas (each weighted on the extention of its surface)? thank you, -stefano

3 5

vertices for mri_label2label using volume registration
by Darren Weber 10 Jul '06

10 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Doug et al., when using mri_label2label with the --regmethod volume, there are no vertices output in the .label file. When loading the .label file into tksurfer, it crashes tksurfer without any error message. It is possible to obtain vertices and to visualize them for the results of mri_label2label when using the volume regmethod? Best, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEra33xaCYN7qs0v4RAkgGAKCNxkYDcQDFCPbu2HCxhSyJPrywDgCfeEua 7Yqo15X8Brb7w5hYssPII5I= =99Kz -----END PGP SIGNATURE-----

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trouble using inorm-sess
by Sebastian Moeller 10 Jul '06

10 Jul '06

Hi List, we have some problems with inorm-sess and some data sets. No matter how we set -tresh (well, 0.1, 0.5, 0.75 or 1.0) some of our functional runs produce errors/warnings. (and the "INFO: no voxels found under thershold" messages, but they look benign). The warning are mostly divides by zero, but they still result in inorm-sess exiting SUCCESSFULLY, they coincide with the INFO... lines so they might be expected. But some of the runs are weirder, they give "??? Subscripted assignment dimension mismatch. \n Error in ==> fast_inorm at 88 \n twf_under(nthslice,:) = mean(y2(iunder,:));" Unfortunatelly looking inside fast_inorm.m does not give me any clue, what is going on. If there is anything I can do to help debug this problem, let me know. BTW the same data can be safely normalized after smoothing (using spatialsmooth-sess). freesurfer 3.0.3 Linux-centos4_x86_64-pub, Matlab 7.1 x86_64, running suse Linux 10.1 ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Re: [Freesurfer] printing out from tksurfer and tkmedit
by Don Hagler 09 Jul '06

09 Jul '06

Here you go. No guarantees of usability or support. >From: Chacko Cherian <chacko_cherian(a)yahoo.com> >To: Don Hagler <dhaglerjr(a)hotmail.com>, fischl(a)nmr.mgh.harvard.edu, >kteich(a)nmr.mgh.harvard.edu >CC: chacko_cherian(a)yahoo.com, freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] printing out from tksurfer and tkmedit >Date: Wed, 5 Jul 2006 16:15:05 -0700 (PDT) > >Thanks Don.That would be really useful. > >Chacko. > >--- Don Hagler <dhaglerjr(a)hotmail.com> wrote: > > > If there is interest, I could post my shell script > > for generating a tcl > > script and running tksurfer (with an option to write > > to rgb). I have > > another one that will render all w files in a > > particular directory (as > > rgb's) and another that will render all frames from > > an mgh (painted surface) > > file (as tif's). > > > > With the older version of tksurfer, you can render > > offscreen, which is > > convenient for batches of files (because otherwise > > your monitor is unusable > > for a long time). > > > > > > >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > >To: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> > > >CC: Chacko Cherian <chacko_cherian(a)yahoo.com>, > > >freesurfer(a)nmr.mgh.harvard.edu > > >Subject: Re: [Freesurfer] printing out from > > tksurfer and tkmedit > > >Date: Fri, 30 Jun 2006 11:39:03 -0400 (EDT) > > > > > >but you could write a tcl script to do it > > automatically > > >On Fri, 30 Jun 2006, Kevin Teich wrote: > > > > > >>>How can I can I print out the display images from > > tksurfer and > > >>>tkmedit other than manually saving them into tiff > > and then printing > > >>>them.IS there any way to print them directly? > > >> > > >>No, sorry, saving TIFFs is the only output that > > tkmedit and tksurfer > > >>do of that kind. > > >> > > >> > > >_______________________________________________ > > >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 > > > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

dependency issue for "tk" related binaries
by apseyed＠bu.edu 08 Jul '06

08 Jul '06

In testing: $ /usr/local/freesurfer/bin/tkmedit /usr/local/freesurfer/bin/tkmedit: error while loading shared libraries: libtix8.1.8.3.so: cannot open shared object file: No such file or directory $ sudo rpm -Uvh glut-3.7-12.i386.rpm itcl-3.2-88.i386.rpm tix-8.1.4-88.i386.rpm /usr/local/freesurfer/bin/tkmedit: error while loading shared libraries: libtk8.4.so: cannot open shared object file: No such file or directory I have tk-8.3.5-92 installed and thus /usr/lib/libtk8.3.so. When i tried to install tk-8.4.5-8.i386.rpm, I ran into a dependency conflict problem: error: Failed dependencies: libtcl8.4.so is needed by tk-8.4.5-8 tcl = 8.4.5 is needed by tk-8.4.5-8 libtk8.3.so is needed by (installed) tix-8.1.4-88 tk = 8.3.5-92 is needed by (installed) tk-devel-8.3.5-92 libitcl3.2.so is needed by (installed) tix-8.1.4-88 libitk3.2.so is needed by (installed) tix-8.1.4-88 itcl is needed by (installed) tix-8.1.4-88 I tried to install tcl-8.4.5-7.i386.rpm, and got another slew of deps: error: Failed dependencies: libtcl8.3.so is needed by (installed) expect-5.38.0-92 libtcl8.3.so is needed by (installed) tk-8.3.5-92 libtcl8.3.so is needed by (installed) tix-8.1.4-88 tcl = 8.3.5-92 is needed by (installed) tcl-devel-8.3.5-92 libitcl3.2.so is needed by (installed) tix-8.1.4-88 libitk3.2.so is needed by (installed) tix-8.1.4-88 itcl is needed by (installed) tix-8.1.4-88 so then i tried to force the install. --nodeps for both of the above. then i tried again: $ /usr/local/freesurfer/bin/tksurfer /usr/local/freesurfer/bin/tksurfer: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory which is included in xorg-x11. after installing xorg: /usr/local/freesurfer/bin/tksurfer: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory so I installed: gsl-1.1.1-5.i386.rpm then: /usr/local/freesurfer/bin/tksurfer: error while loading shared libraries: libitk3.2.so: cannot open shared object file: No such file or directory which I already installed, and when i installed again, it is asking for libtk8.3.so again, which was overridden with nodeps. Now, I installed the version 3.0.3 that said is compatible with redhat 9, which is close to what I am running, can you offer any suggestions? Thanks, Patrice

2 2

recon-all exited with errors
by Nandita Shetty 07 Jul '06

07 Jul '06

Hi, I came across an error in the third stage of reconstruction using freesurfer. The images,scripts etc are at space/megraid/42/ACE/PILOTDATA/DATA_PROCESS The recon log says that recon-all exited with errors and stopped at Surf Reg rh. I am a new user and was hoping that you could help me out with the same. Also, I do know that the inflated brain is not ideal but nevertheless wanted to complete the reconstruction to get a feel of it. This is what the error log says MRISreadVertexPosition(smoothwm): could not open file ../surf/rh.smoothwm MRISreadOriginalProperties: could not read surface file smoo Thanks in advance for any help in this regard.

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