Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

Feedback on Talairach QA and Q about segmentation in several atrophy
by Damian Jenkins 30 Apr '08

30 Apr '08

Using the -notal-check flag after recon-all to bypass Talairach allowed us to reclaim several images for inclusion in a study containing MS patients with severe atrophy. However, one image (which is nearly all ventricle!) is proving difficult to segment. The segmentation process parcels up bits of the ventricular space as thalamus and as caudate. Is there a way around this, or do images with very severe atrophy need to be excluded? Dr Damian Jenkins Department of Clinical Neurology Oxford University

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can not see the pial surface using tksurfer
by yczhang 30 Apr '08

30 Apr '08

Hi, when I launched the command tksurfer to see the constructed pial surface, only a very small part of the surface can been seen in the window. I do not know how to fix the problem. Thanks! yczhang 2008-04-25

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WM volume estimation - image capture
by Damian Jenkins 30 Apr '08

30 Apr '08

Whilst estimating white matter volume using mris_wm_volume is it possible to save an image for inspection? Dr Damian Jenkins Department of Clinical Neurology Oxford University

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Re: [Freesurfer] White Matter Regional Volumes
by Jenni Pacheco 30 Apr '08

30 Apr '08

Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward. Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 8:17 AM, Jenni Pacheco <jenni.pacheco(a)gmail.com> wrote: > Hi Jen, > > In Doug's absence, let me try and give you the best answer I can! The > wmparc.mgz uses the cortical parcellation and grows each label down through > the white matter - giving a label of the white matter underneath each > cortical unit. Because of this there will be both cortical (ctx) and white > matter (wm) measures in the wmparc.stats - the ctx regions being taken > directly from the cortical parcellation, and the wm regions resulting from > growing those inward. > > Depending on what version you are using, you can use asegstats2table to > tabulate these results, as you would the subcortical segmentation. Check > the help on this file, there may be an option to do it directly, or you may > have to use a flag to specify a new stats table (i.e., wmparc.stats instead > of aseg.stats). > > Hope this is helpful, > Jenni > > > On Wed, Apr 30, 2008 at 7:04 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > > Hi Jen, > > > > Doug is out of town at the fBIRN meeting, and he's the one that will > > answer this so you might have to wait a bit. > > > > cheers, > > Bruce > > > > On Tue, 29 Apr 2008, Jennifer Bramen wrote: > > > > I posted the below question regarding white matter volumes to the list > > > last Friday. I think it fell through the cracks because I sent it out in the > > > late afternoon, and was hoping someone could help me understand 1) the > > > outputs of indicvidual wmparc.stats files and 2) how to tabulate these data > > > like we can with gray matter volumes. Thanks again. > > > > > > Jen > > > > > > Hi Freesurfer Users, > > > > > > > > This may be a newbie question. I am trying to evaluate regional > > > > volumes. I have been able to tabulate the gray matter volumes, but cannot > > > > figure out how to tabulate all the white matter volumes. I see that in > > > > individual folders, there is a file called wmparc.stats. Do any of the tools > > > > query this file, or will I need to pull the data manually? Inside this file, > > > > I see some of the regions listed as wm-?h-<regionname>. Next to these are > > > > sometimes a lot of zeros and sometimes a bunch of values. I am wondering why > > > > so many of these do not have values associated with them. I am also > > > > wondering why only some of the regions listed in this file are labeled wm, > > > > when the file suggests it contains white matter stats... > > > > > > > > If there is somewhere on the site that explains white matter > > > > volumetric analyses, could someone please send me the link? > > > > > > > > Thank you > > > > > > > > Jennifer Bramen > > > > > > > > ---------------------------------------------------------- > > > > IMPORTANT WARNING: This email (and any attachments) is only > > > > intended for the use of the person or entity to which it is addressed, and > > > > may contain information that is privileged and confidential. You, the > > > > recipient, are obligated to maintain it in a safe, secure and confidential > > > > manner. Unauthorized redisclosure or failure to maintain confidentiality may > > > > subject you to federal and state penalties. If you are not the intended > > > > recipient, please immediately notify us by return email, and delete this > > > > message from your computer. > > > > ---------------------------------------------------------- > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > ---------------------------------------------------------- > > > IMPORTANT WARNING: This email (and any attachments) is only intended > > > for the use of the person or entity to which it is addressed, and may > > > contain information that is privileged and confidential. You, the > > > recipient, are obligated to maintain it in a safe, secure and confidential > > > manner. Unauthorized redisclosure or failure to maintain confidentiality may > > > subject you to federal and state penalties. If you are not the intended > > > recipient, please immediately notify us by return email, and delete this > > > message from your computer. > > > ---------------------------------------------------------- > > > > > > _______________________________________________ > > > 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 > > > > > > -- > Jenni Pacheco, MA > Learning and Memory Lab > The University of Texas at Austin > Department of Psychology > 1 University Station A8000 > Austin, TX 78712 > phone: (512) 471-2727 > fax: (512) 471-5935 > email: jpacheco(a)mail.utexas.edu -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: jpacheco(a)mail.utexas.edu

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Cannot execute any freesurfer GUI- Error of failed request:
by Jennifer Bramen 30 Apr '08

30 Apr '08

FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-stable-pub-v4.0.3 Kernel info: Darwin 9.0.0 i386 ___ I recently updated to the newest release of freesurfer because for some reason I was unable to run qdec with 4.0.2. Though it appears that everything is setup exactly as it was before, I cannot execute any of the GUI (tkmedit, tksurfer, or qdec) I tried using the tutorial dataset to debug this. Below is an example command: tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Regardless of what I try to run, I get the following error: Couldn't create output file .xdebug_tkmeditX Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 17 Current serial number in output stream: 17 I already looked in the archives. I do have the most up to date version of X11. I am running this on my local machine, not via ssh, so this is not a display problem. All of my necessary variables are set (SUBJECTS_DIR, FREESURFER_HOME) and I have sourced $FREESURFER_HOME/ SetUpFreeSurfer.csh. Thnaks you in advance for your help. Jennifer Bramen ---------------------------------------------------------- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. ----------------------------------------------------------

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Unknown error
by Jerry Yeou-Wei Chen 29 Apr '08

29 Apr '08

Hello, I am having trouble deciphering why I got the error attached below. Any suggestions would be greatly appreciated! Thanks, - Jerry Tue Apr 22 10:15:22 EDT 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Apr 22 10:15:23 EDT 2008 /scratch/freesurfer/subjects/17/s017/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7072, pval=0.4932 >= threshold=0.0050) awk -f /scratch/freesurfer/bin/extract_talairach_avi_QA.awk /scratch/freesurfer/subjects/17/s017/mri/transforms/talairach_avi.log TalAviQA: 0.96840 z-score: -2 #-------------------------------------------- #@# Intensity Normalization Tue Apr 22 10:15:23 EDT 2008 /scratch/freesurfer/subjects/17/s017/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.976 0.083 0.030 -136.866; -0.072 1.053 0.164 -153.262; -0.020 -0.109 1.085 -122.101; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 19 minutes and 44 seconds. white matter peak found at 111 gm peak at 88 (88), valley at 80 (80) csf peak at 57, setting threshold to 77 white matter peak found at 111 gm peak at 88 (88), valley at 80 (80) csf peak at 55, setting threshold to 77 #-------------------------------------------- #@# Skull Stripping Tue Apr 22 10:35:16 EDT 2008 /scratch/freesurfer/subjects/17/s017/mri mri_em_register -skull nu.mgz /scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/scratch/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 using (102, 110, 122) as brain centroid... mean wm in atlas = 126, using box (80,83,98) --> (123, 136,146) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux kdavis8-efef.uhnres.utoronto.ca 2.6.23.1-21.fc7 #1 SMP Thu Nov 1 21:09:24 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Apr 22 10:41:40 EDT 2008

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Re: [Freesurfer] VNC/GLX... what is really vncserver.glx
by Tsung-Ren Huang 29 Apr '08

29 Apr '08

Hi Yaroslav, You can comment out those lines regarding GLoverride. The real magic, as pointed out by Nick, is acutally the xf4vnc that can be downloaded from http://sourceforge.net/projects/xf4vnc . Tren > On Mon, 2007-01-15 at 23:27 -0500, Yaroslav Halchenko wrote: > Thank you very much for providing the script. Now the question is what > magic do you keep under /usr/lib64/GLoverride:/usr/lib/GLoverride > because the rest of the script seems to be close to the standard > vnc server script shipped originally (Debian maintainer introduced some > changes as well but most only for parameter/configuration > specifications). >> On Tue, 16 Jan 2007, Nick Schmansky wrote: >> Yaroslav, >> If you goto that RemoteAccess wiki page, and click on 'vncserver.glx', >> it will now allow you to download that script. You will have to modify >> it a bit: look for instances of /usr/pubsw/packages, which point to our >> installation of VNC. >> Nick

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fix for qdec 'Bad Match' error
by Nick Schmansky 29 Apr '08

29 Apr '08

For those who are unable to run the 'qdec' app because it exits with a 'Bad Match' error, there is a new fix you can try. Put this text: Section "Extensions" Option "Composite" "false" EndSection at the end of your /etc/X11/xorg.conf file. You will need root privileges to make this edit. This seems to work for ATI graphics cards. For NVidia, try replacing the word 'false' with 'Disable'. If qdec opens for you already, you don't need this fix. Note that you should no longer need to 'setenv XLIB_SKIP_ARGB_VISUALS 1', which means that images should render using hardware acceleration (assuming your driver and X windows implementation supports that). It's not known what impact disabling the 'Composite' function of the driver will have on other applications, but it seems it has been disabled in RHEL 4 and earlier Linux variants, but is enabled in later (5,6,7, Ubunutu), which is why the problem appears in those. Another note, this doesn't address the problem with tksurfer not displaying the surface on ATI cards, although I have found the v.33 of the driver works. Nick

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lh.aparc.a2005s: S_subcentral_ant label
by Juranek, Jenifer 28 Apr '08

28 Apr '08

We recently started playing with the ?h.aparc.a2005s annotation files (fsv401). We noticed that in /freesurfer/subject/bert, the S_subcentral_ant label is not listed as a variable in the /stats/lh.aparc.a2005s output file. However, this variable name does *sometimes* appear in some of our study subjects. 1) Is this normal behavior? 2) Is it possible to add a FieldName index (analagous to the aseg.stats file) to facilitate detailed accountings of "empty" variables in the ?h.aparc.a2005s files? Many Thanks for any information you can provide, Jenifer

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installation
by Lars M. Rimol 27 Apr '08

27 Apr '08

Hi, I downloaded the freesurfer-Linux-rh9-stable-pub-v4.0.3-full, and I followed the instructions on your website ( http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-platform-releas… ): 1) extract to /usr/pubsw/packages/ 2) place the license file in the resulting /usr/pubsw/packages/freesurfer 3) type recon-all --help When I did (3) I got text about FreeSurfer, so far so good, but if I try to start tksurfer og tkmedit, I get: tksurfer.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory mris_preproc mri_surf2surf mri_glmfit all seem to work, i.e. I get the normal help text when I type the commands without any further input What should I do next? Thank you! -- yours, LMR

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Freesurfer April 2008