Freesurfer December 2007

freesurfer@nmr.mgh.harvard.edu

45 participants
74 discussions

Qdec with v3
by Michael Harms 20 Dec '07

20 Dec '07

Hello, We are getting ready to do some surface analyses on data processed under v3.0.4 or v3.0.5. We would like to try using the Qdec utility from FS v4 to analyze this v3 data. Is that a legitimate thing to do? I see that at a minimum, we will need to run recon-all -s <subj> -qcache (under FS v4) to generate necessary files expected by Qdec. The various surfaces for the 'fsaverage' subject differ between v4 and v3. Obviously, running -qcache under v4 will use the v4 'fsaverage' subject. Provided we then also link to the v4 'fsaverage' subject for display purposes, I'm assuming that we'll be in proper correspondence. Is that correct? v3 and v4 also have different .gca and .gcs atlases. But I don't need to worry about that in terms of using Qdec, right? Is there anything else I'm missing that would need to be done, or why Qdec (v4) can't be used on v3 processed data? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Fixing a bad talairach
by Caroline Chapman 19 Dec '07

19 Dec '07

Hi Freesurfers, Happy Holidays! I have a subject failing at Intensity Normalization, and upon checking the talairach, I found that it is very bad. When loaded in tkregister2, the talairach is off the screen, and the orientation is off--coronal is matched to saggital). According to the wiki instructions, I will need to correct the transform. Is it possible to fix this bad talairach in tkregister2? If it is helpful, I have the error message from the Intensity Normalization error printed below. Thank you! Caroline mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.484 1.141 -0.183 -61.600; -1.154 0.466 -0.149 -62.214; -0.067 0.226 1.231 276.948; 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 Linux node0072 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Tue Dec 11 15:16:05 EST 2007 -- Caroline Chapman Research Assistant/Technician Massachessetts General Hospital Geriatric Research, Education and Clinical Center VA Boston Healthcare System (857)364-2093 chapman(a)nmr.mgh.harvard.edu

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ENC: Re: Optimizing FreeSurfer
by Pedro Paulo Oliveira Jr 19 Dec '07

19 Dec '07

Hello, I have a couple of questions, not so technical. A) In your opinion what would be the best measure for comparing number of neurons among subjects: Average cortical thickness or Volume of White matter. B) Automatic parcelation and atlas based segmentation is a valid approach for patients with severe cortical malformation? Thanks in advance for your help. Best Regards Pedro Paulo Jr.

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fsl + freesurfer
by Gui Xue 19 Dec '07

19 Dec '07

Hi-I am trying to work out a work flow of integrating fsl and freesurfer. the basic goal is to do surface-based group analysis. what I have now is the run1.feat, run2.feat and mean.gfeat for each subject done by FSL Feat and the processing anatomy using recon-all in freesurfer. so the question now is how to combine them. It seems to me that one way is to (1) use reg-feat2anat to register the feat to freesurfer anatomy; (2) using mris_preproc to resample it into common surface space, and (3) using mri_glmfit to computer the mean for each subject; and repeat (2) and (3) for group analysis. but if I want to use feat to do the whole statistics, I am not sure how should I proceed. I will still use (1) to do the registration, and use (4) feat2surf to resample each feat into common surface space. but then I am not sure how to do statistics using Feat (both fixed effect to combine two runs and random effect to combine across subjects). any help will be greatly appreciated. Gui

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the unknown zone in the average
by Wang, Xin 19 Dec '07

19 Dec '07

Hello, Group, We calculate the globe mean of thickness by using mris_convert -c lh.thickness lh.white lh.thickness.asc mris_convert -c rh.thickness rh.white rh.thickness.asc and then merge two .asc files to calculate the average Does this procedure include the neocortex only, or also include some spots in the unknown zone that also have readings in the thickness map? If the unknown zones are included how to exclude them? we processed the data with the version prior to 4.0.1. Thank you in advance, XIn Wang

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mris_anatomical_stats
by Gallo, Antonio (NIH/NINDS) [F] 18 Dec '07

18 Dec '07

Hi All, Could you please help with the following: When we run mris_anatomical_stats with FS 4.0.1 we can see the results on the terminal and we are able to get a log file, but this latter appears always blank. Countrarywise, when we use mris_anatomical_stats with FS 3.0.5 on the same set of data we are able to get a log file with the outputs but we have noticed these two things: 1) results are not identical to the ones coming from mris_anatomical_stats with FS 4.0.1; in particular, we see minimal differences when looking at the average cortical thickness and major differences when looking at the three last measures (i.e. average integrated rectified mean curvature, average integrated rectified Gaussian curvature, folding index); 2) the results reported in the in the log file for the total surface area always the ones coming from the pial surface whatever surface name we specified (pial or white) Thanks in advance for your help, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5C203B Bethesda, MD, 20892 - USA ph #: 001-301-496.7368 fax #: 001-301-402.0373 ***********************

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hole in pial surface
by Matt Colvin 18 Dec '07

18 Dec '07

Dear Freesurfer gurus: I have come across two brains which appear to have small holes in the pial surface when viewed in tkmedit. Each hole appeared for only one slice. Performing mris_euler_number on all the appropriate surfaces yielded no aberrant results (ie, =2, no defects). Further, there didn't appear to be anything wrong with the surfaces when viewing the same spots in tksurfer. Curiously, both holes were in the right temporal lobe. I have attached screen captures of both holes. Is this simply a visualization problem that I should ignore? Or is there some other check we need to perform? Thanks in advance for any help that anybody is able to give. --Matt Colvin

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Re: [Freesurfer] qdec BadMatch error
by Pedro Paulo 18 Dec '07

18 Dec '07

Hi Lisa, I have found a solution for your problem: Before running Qdec, execute: export XLIB_SKIP_ARGB_VISUALS=1 It will fix this problem until Ubuntu and NVidia resolve the open issue with GLX. Best Regards, Pedro Paulo Jr --------------------------------------------------------------------------------------- Lisa, Unfortunately, this is a problem that I have not been able to recreate locally with the operating systems I have available. It seems to occur just on Ubuntu. Have you tried updating the video driver? That is the only thing I can think to try. I will try to google-search this problem to find a solution. Nick On Sun, 2007-09-16 at 10:29 +0100, Lisa Ronan wrote: > Hi All, > > I am having the same problem as outlined previously by Andrew, namely > a problem loading qdec in Ubuntu Feisty > > Reading /home/freesurfer/lib/tcl/tkUtils.tcl > Using /home/freesurfer//lib/tcl/fsgdfPlot.tcl > X Error of failed request: BadMatch (invalid parameter attributes) > Major opcode of failed request: 66 (X_PolySegment) > Serial number of failed request: 5049 > Current serial number in output stream: 5052 > > Any ideas as to how to resolve it? > > Many thanks in advance, > > Lisa Ronan > Brain Morphometry Lab > Beaumont Hospital > Dublin 9 > Ireland > > > On 8/21/07, Andrew Reid <[EMAIL PROTECTED]> wrote: > Hi, > > Just installed version 4.0.0 and tried to execute qdec. When I > do so I > get the following error. Any ideas what it means and how to > remedy it? > > > Reading /home/typically/freesurfer/lib/tcl/tkUtils.tcl > Using /home/typically/freesurfer/lib/tcl/fsgdfPlot.tcl > X Error of failed request: BadMatch (invalid parameter > attributes) > Major opcode of failed request: 66 (X_PolySegment) > Serial number of failed request: 4721 > Current serial number in output stream: 4724 > > I am using Ubuntu Fiesty. > > Thanks in advance, > > Andrew Reid > Department of Neurophysiology and Neuroinformatics > UMC St. Radboud > Nijmegen, The Netherlands > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ubuntu recon-all
by Roberto Roiz Ssantiáñez 18 Dec '07

18 Dec '07

Dear all, I have just installed freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz on Ubuntu 7.10. I have tried to test the installation and after sorting out some problems with the video card drivers, I obtain the following message when trying to run "recon-all -s bert -autorecon1": *roberto-desktop:/usr/local/freesurfer> sudo recon-all -s bert -autorecon1 *sudo: recon-all: command not found *roberto-desktop:/usr/local/freesurfer> However, when I run "recon-all --help | less" everything looks ok. Anyone having the same problem? Thanks in advance Roberto Roiz Santiañez

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tkmedit-sess result
by anisha narula 17 Dec '07

17 Dec '07

Hello, I am doing a retinotopy analysis and when I perform the sliceview-sess command, I get activation in the areas of interest. I used the tkmedit-sess command *tkmedit-sess -analysis rtopy -contrast eccen -map h -sf sessid -df sessdir -volid orig.mgz* however there is no activation. I have attached the image above. Thank You

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Freesurfer December 2007