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30131 discussions

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

2 1

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.

4 8

[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/

3 5

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.

2 1

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 > >

2 1

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

3 2

RE: [Freesurfer] tksurfer display problems
by Wang, Xin 19 Nov '08

19 Nov '08

We did for one node, and going to up-grade the rest. A simple answer to your question is to up-grade any node you want to run tksurfer. Help it helps. Xin ________________________________ From: Siddharth Srivastava [mailto:siddys@gmail.com] Sent: Wed 11/19/2008 6:37 PM To: Wang, Xin Subject: Re: [Freesurfer] tksurfer display problems Hi Xin, Thanks for the reply. I am contacting you since you mentioned that you are running freesurfer on a cluster. I contacted my sysad regarding this problem, and they want to know if this upgrade has to be dome on every node of the cluster. can you recommend something regarding this? best regards, sid. On Wed, Nov 19, 2008 at 11:46 AM, Wang, Xin <Xin.Wang(a)utoledo.edu> wrote: We just solved the same problem by upgrading the driver of video card on the cluster. An early massage in the freesurfer archive gives more details. Xin ________________________________ From: Siddharth Srivastava [mailto:siddys@gmail.com] Sent: Wed 11/19/2008 1:21 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer display problems Hi mjp, Thanks for an account of a working solution to the problem. I just wanted to know if this intervention has to done on the client machine (from where i am viewing the results), or on the server side (on which i am processing the data)? Further, in case of a 64 bit machine, would the source and the destination directories change accordingly? best regards, sid. On Wed, Nov 19, 2008 at 8:50 AM, Mark J. Pearrow <mjp(a)mit.edu> wrote: Hi all, This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted server. I found this posting: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.ht… Which seemed to indicate that it was not the card itself that made the difference, but rather some software component that made things work. There is an extension to X11, called GLX, which allows the remote side (the "client", in X11 speak) to bypass the processing of OpenGL commands and to send them to the server. So, following the advice in the posting above, I downloaded the latest NVidia.run package and unpacked it by using the "-x" flag - then I copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. Then I ran "ldconfig -v" to update the ld cache. And voila, I can run tksurfer over X11, VNC and NX now on a server that has no NVidia card, without any problems. I still don't understand what exactly is being provided by NVidia's version of the libraries, but I suspect it has to do with "TLS" (in the context of OpenGL, not in the crypto sense). This appeared in the output of `ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken system after I installed those files: libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 mjp On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote: Hi Sid, this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC. cheers, Bruce On Tue, 18 Nov 2008, Siddharth Srivastava wrote: 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Version Discrepancies in Cortical Thickness Analysis?
by Ryan Scotton 19 Nov '08

19 Nov '08

Hi Bruce, My team has recently begun planning for data analysis after completing the overwhelming majority of our FreeSurfer runs and manual edits. However, it came to my attention that we do not currently have Qdec installed on our system...I realized that this is because we were using a very outdated version of FreeSurfer (3.0.4) that did not include Qdec. We have since downloaded the newest version so that we can begin data analysis, but this raises a bigger question: is it necessary for us to rerun FreeSurfer on all of our subjects (250+) if we are ONLY concerned with the white matter/grey matter surfaces and cortical thickness measurements? If not, spectacular. If so, is there only a small portion of the recon-all stream that we could run so that we could take care of this problem as fast as possible? Thanks! Ryan

3 2

Issues with FreeSurfer and Slicer3
by joel bruss 19 Nov '08

19 Nov '08

I must have posted this to an incorrect address before so I'll try this again: Hello- I'm running freesurfer-Linux-centos4-stable-pub-v4.0.5 on Suse 11. I've used the output of FreeSurfer, specifically wmparc.mgz to create a 32-bit volume to which I've applied edits. The two commands I used were: mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o wmparc-in-native.mgz --regheader --interp nearest mri_convert --in_type mgz --out_type analyze wmparc-in-native.mgz wmparc_in_native_analyze (The new Analzye set was renamed FSParcel.hdr/img) After making the appropriate edits, I wanted to put this file back into mgz format/freesurfer space so I ran: mri_convert --in_type analyze --out_type mgz FSParcel 3065_FSParcel.mgz mri_vol2vol --mov FSParcel.mgz --targ mri/wmparc.mgz --o FSParcel_FSorient.mgz --regheader --interp nearest (I assumed that a target of wmparc would be most appropriate sinc that's what I started with but I've tried aseg as well) I've been playing around with Slicer and trying load the file as a label file to which I create (I believe) vtk models. If I convert wmparc to an Analyze set and then back to FreeSurfer mgz without any edits, I get an exact copy, as would be expected. If I make any alterations to the file and follow my steps, Slicer gripes that it can't parse the header. No matter what dims I use, I get pixels scattered across the screen and it appears that the volume is scrunched to 1 slice. If I run tkregister (as mri_vol2vol suggests) tkregister2 --mov FSParcel_FSorient.mgz --targ $SUBJECTS_DIR/sub1/mri/aseg.mgz --reg FSParcel_FSorient.mgz.reg everything looks fine. I find the Slicer documentation a bit lacking and don't know who to turn to. Is there something inherently wrong with my commands or is there a way to write header params to the mgz file so that Slicer will just work? -Joel

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