Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

design is ill-conditioned
by Maximilien Chaumon 13 Jan '10

13 Jan '10

Hi freesurfers, I'm trying to run an estimation with my last subject and get stuck with a ERROR: design is ill-conditioned I can imagine this means that my design misses something bu I can't find what. Conditions all have events in all runs, time points are equally spaced. Here's the log of the session /autofs/space/bomba_016/users/chaumon/log/selxavg3-sess-bold-Analyse_Simple_Confidence-091215135329.log Thanks for any help, Max

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poll question: Mac OS Tiger users
by Nick Schmansky 13 Jan '10

13 Jan '10

for the Mac OS users out there: who still needs a Tiger OS build of freesurfer? and on what processor (intel or ppc)? i'd like to discontinue support for Tiger (and redirect efforts toward working with Snow Leopard), but if enough people still need the Tiger build then we can keep our creaky-old machine around to do this. Nick

1 1

a freeview bug ?...
by Gonzalo Rojas 13 Jan '10

13 Jan '10

Hi: I load orig.mgz using freeview application, but when I try to load lh.thickness or rh.thickness file, freeview quits unexpectedly... it is a freeview bug ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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a freeview bug ?...
by Gonzalo Rojas 13 Jan '10

13 Jan '10

Hi: I have freesurfer 4.4.0... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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modification of tksurfer and tkmedit palettes
by Gonzalo Rojas Costa 13 Jan '10

13 Jan '10

Hi: I will write my question in another way: in which file could I find the palette that tksurfer and tkmedit uses to display overlay data ?... because I want to create other palettes... Sincerely, Gonzalo Rojas Costa

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tkmedit and tksurfer volume display problem in Ubuntu 9.04
by Miguel Burgaleta 13 Jan '10

13 Jan '10

Hi again, I am experiencing some problems when testing my freesurfer installation in Ubuntu 9.04. When I run tkmedit and tkmsurfer the interface opens OK, but the volume display window behave in a weird manner in both cases: it appears but quickly disappears. In tkmedit, if I click on some of the buttons to choose a view (for instance, axial), the volume window appears but it disappears if I move the cursor out of the selected button. Is this problem familiar to anyone? Thanks in advance for any help! Miguel

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Freesurfer Ubuntu 9.04 installation
by Miguel Burgaleta 13 Jan '10

13 Jan '10

Dear all, This is a technical, linux-related question: I have just installed Freesurfer in a computer running Ubuntu 9.04. When testing the installation, I get an error message right in the first step. I try to do: tkmedit bert orig.mgz And the message I get is: tkmedit.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory I was wondering if some of you experts can say how to solve this? Thanks a lot in advance, Miguel

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unknown error
by Xiantong Zhen 13 Jan '10

13 Jan '10

Hi experts, I run freesurfer to compute the thickness, but I find some subjects failed with error. Would you please tell me how to handle this error. Thank you very much! And the error is as follow: .................................................................................... talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6987, pval=0.4932 >= threshold=0.0050) awk -f /public/home/users/lzuxucl/freesurfer/bin/extract_talairach_avi_QA.awk /public/home/users/lzuxucl/subjects/S45260/mri/transforms/talairach_avi.log TalAviQA: 0.94844 z-score: -6 ERROR: Talairach QA check failed! z-score = -6 <= -6 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer..nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux node5 2.6.9-55.ELsmp #1 SMP Fri Apr 20 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jan 11 15:52:39 CST 2010 Best, Xiantong

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(no subject)
by Guang Zeng 12 Jan '10

12 Jan '10

Recently, I sent several emails to ask the same kind of question about building our own template and atlas. Thanks a lot for the quick replies, they helps me a lot. Currently, I still have a question about building our own atlas using mris_ca_train, sorry to bother again. In our lab, we have a labeled surface atlas, we'd like to use this atlas instead of using FS's desikan_killiany.2007-06-20gcs. It is kind of difficult for us to load every subject in our training set to tksurfer, and manually label each ROI based on our ATLAS. >From what I learned from your replies, I did the follwoing steps to creat our own atlas, Step# 1 Select a subject, and then send it to oue ATLAS Toolbox for automatic segmentation and parcellation Step# 2 Sample the volume segmentations onto the surface Step# 3 Convert the sampled segmentations to an annotation file I applied those three steps to 59 subjects seperately, got .annot file for each of them, then I called the mris_train, my command line is: mris_ca_train -n 2 -t /home/freesurfer/ATLASColorLUT.txt lh sphere.reg myatalas.annot $subjects_list lh_myatlas.gcs My results are shown in the attached .ppt file, my question is: If we looked at Fig. 1(b) and Fig. 2 (b). There are no labels around the ventricl areas in my training set, while when the built atlas was loaded to average subject, that area was labled. If there are a way to avoid this problem and improve my atlas? Do I use the wrong command ? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/

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thickness map from a label
by Ritobrato Datta 12 Jan '10

12 Jan '10

Hello All, I have created some surface labels and want to create corresponding thickness maps (Not stats). Is there a way to do that ? Thanks Ri

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Freesurfer January 2010