Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

White matter surface edits
by Martin Ystad 24 Nov '08

24 Nov '08

Hi, I have been trying to make freesurfer include all of my white matter in the wm-surface. It seems to run directly across some of the gyri in my brain volume (see attached picture). I first tried to add control points at the base of the gyri, and then along the gyri, but that did not seem to have much effect. Then I manually drew the white matter onto the wm.mgz-volume (see attached picture), but that did only help for some of my gyri. Do you have any tips on how to force freesurfer to include the remaining white matter in the wm surface? Thanks, Martin Ystad

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stats in freesurfer
by Lúcia Garrido 24 Nov '08

24 Nov '08

Dear all, I have a few questions about stats in freesurfer that I'd be very grateful if you could answer. 1. Is it possible to reduce the search from the whole brain to a smaller region of interest to apply corrections for multiple comparisons? For example, if I'm interested in differences in the fusiform gyrus, can I restrict the FDR correction to the fusiform? 2. Is it important to control for any global measure when comparing cortical thickness? For example when comparing grey matter volume, it's good practice to control for the intracranial volume. In case of cortical thickness (and other dependent measures in freesurfer), do you know how these are affected by the intracranial volume (or other measures) and how these could be controlled? 3. Finally, I posted a question a few days ago about comparing volume using freesurfer. I'm sorry for insisting on this but I still haven't found any response. My question was whether it's possible to compare volume maps in freesurfer. I'm using an older version (4.0.4) and my impression is that the most recent version might have this feature, but this is unclear to me. I'd be very grateful if you could let me know if this is the case. And if there's any way in which I can compare volumes usig data pre-processed using the version I have. Thank you very much! Best wishes, Lucia

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Hi, a problem!
by Zhangyuanchao 23 Nov '08

23 Nov '08

Using lgi, I want to know whether I should mask out the corpus callosum and the structures which lies below the corpus callosum as I do it using thickness measure. Thanks! ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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mri_ca_train: CGAupdateNodeCovariance
by Jason S. Minamora 23 Nov '08

23 Nov '08

I got the following output after running the second stage of `rebuild_gca_atlas.csh', which starts by training on all segmented subjects. The first stage (which performs a Tal reg on the first subject listed in env var $SUBJECTS) finished without problems: echo "$train using all subjects, using ${M3D_ONE}, producing ${GCA}..." set cmd=($train -prior_spacing 2 -node_spacing 4 -mask ${MASK_VOL}) set cmd=($cmd -parc_dir ${SEG_VOL} -xform ${M3D_ONE} -T1 ${T1_VOL} -check) set cmd=($cmd ${SUBJECTS} ${GCA}) --------- Execution stopped after this step: --------- (STDOUT) computing covariances for subject A59, 1 of 4... reading volume /Users/jsm/work/subjects/A59/mri/brain.mgz for masking... gunzip -c /Users/jsm/work/subjects/A59/mri/transforms/talairach_one.m3z GCAupdateNodeCovariance(10, 35, 23, 4): could not find label --------- Here `$SUBJECTS' was set to 'A59 A62 f18 f20', with "A59" being the first subject. Thanks in advance, Jason

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Recon 1
by Kelly Silva 22 Nov '08

22 Nov '08

Hello, I´m having troubles with Autorecon1 of one subject and the script is attached. Thanks, Kelly Atalaia Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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tksurfer display problems
by Siddharth Srivastava 21 Nov '08

21 Nov '08

Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated). This small patch responds to all commands from the GIU, but that is all that i see. I have trawled through the archives, both old and new, and there have been references to similar problems, without any definitive way to solve it. What exact aspect of the system configuration has to be examined/re-worked to solve it? Does anyone have any experience with this kind of problem? with regards, sid.

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[Freesurfer] freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0-full.tar.gz, libexpat.so.0, Gentoo Linux x86_64
by Volkmar Glauche 21 Nov '08

21 Nov '08

Dear all, I've downloaded the latest freesurfer version (4.1.0) for x86_64 Linux. There seem to be some issues with libexpat.so.0, which is no longer available on my Gentoo linux systems. The following files in freesurfer/bin depend on libexpat: freeview.bin libexpat.so.0 => not found libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00002ac5281a8000) mris_volmask.bin libexpat.so.0 => not found orient_mri.bin libexpat.so.0 => not found qdec.bin libexpat.so.0 => not found scuba2.bin libexpat.so.0 => not found I have scanned the freesurfer mailing list archives and got the impression that freesurfer 4.0.4 and above should not depend on depend on libexpat.so.0 anymore. I would be glad if someone could shed some light on this issue. Yours, -- Volkmar Glauche - Department of Neurology volkmar.glauche(a)uniklinik-freiburg.de Universitaetsklinikum Freiburg Phone 49(0)761-270-5331 Breisacher Str. 64 Fax 49(0)761-270-5416 79106 Freiburg http://fbi.uniklinik-freiburg.de/

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cortical labeling issue
by tmazzocc＠artsci.wustl.edu 21 Nov '08

21 Nov '08

Hello all- I'm having some trouble with sessions in which the pial surface is not matching up with the cortical segmentation. Subjects were run on a 1.5T Vision scanner and we're using an average of 3 MPRAGEs. Does anyone have any suggestions on how to troubleshoot this issue? I've attached a snapshot illustrating this problem. Thanks, Tessa These materials are private and may contain Protected Health Information. 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 email.

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Recon/normalization question
by Dashkoff, Jonathan David 21 Nov '08

21 Nov '08

> Hello, > > We are having some trouble with autorecon1, specifially the watershed step. > Here's the error we get: > > > > #-------------------------------------------- > > #@# Skull Stripping Tue Nov 18 15:19:59 EST 2008 > > /autofs/space/madrc_007/users/adeluca/RETRRO_structural/RETRRO_20_old/mri > > > > mri_watershed -T1 -brain_atlas > > /usr/local/freesurfer/stable4/average/RB_all_withskull_2008-03-26.gca > > transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz > > > > > > Mode: T1 normalized volume > > Mode: Use the information of atlas (default parms, --help for > > details) > > > > ********************************************************* > > The input file is T1.mgz > > The output file is brainmask.auto.mgz > > If this is incorrect, please exit with CTL-C > > > > Weighting the input with atlas information before watershed > > > > *************************WATERSHED************************** > > Sorting... > > first estimation of the COG coord: x=128 y=108 z=113 r=76 > > first estimation of the main basin volume: 1871279 voxels > > > > > > > > ******************************************* > > *********************************************** > > *********************************************** > > White matter intensity 0 is lower than CSF intensity 18. > > Please examine input images. Will terminate ... > > *********************************************** > > *********************************************** > > *********************************************** > > > > ********************************************************** > > MRIstripSkull failed. > > ************************************************************ > > Linux aubz 2.6.18-92.1.10.el5 #1 SMP Tue Aug 5 07:42:41 EDT 2008 x86_64 > > x86_64 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Tue Nov 18 15:20:09 EST 2008 > > > Looking at the input file (nu.mgz) it is obvious that the qcquired image isn't > as good as it could be. Looks like there is moderate white matter burden, > dropout on the ventral side of the scan, and some artifacts possibly made > because of dental implants. > > Are there any other steps that can be taken besides marking control points and > adding the -f flag to mri_normalize? > > Thanks, > Jon > >

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volumetric analysis with different versions
by Jared Price 21 Nov '08

21 Nov '08

Hi freesurfer gurus, I just noticed that version 4.1.0 is out. We have a relatively large amount of data already processed through various freesurfer versions such as 4.0.0 4.0.2 4.0.5. Is it valid to compare volumetric measurements from the subcortical segmentation file aseg.mgz across these versions? Must we do reruns? Cheers Jared

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Freesurfer November 2008