Freesurfer

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30076 discussions

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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right choroid plexus missing
by Mishkin Derakhshan 14 Dec '07

14 Dec '07

Hi, Is there any reason why aseg.stats only has a label for the left-choroid-plexus (id 31) and none for the right? I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 thanks, mishkin

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mri_convert options
by Mishkin Derakhshan 14 Dec '07

14 Dec '07

Hi, I am having troubles getting the right options with mri_convert. I ran: recon-all -autorecon1 -i original.mnc -s subj1 recon-all -subcortseg -s subj1 I now want to convert aseg.mgz into aseg.mnc but in the same space and with the same orientation as my original.mnc file. My original.mnc file has the following attributes: double zspace ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:step = -0.9765625 ; zspace:start = 127.418768256005 ; zspace:direction_cosines = -0.0275245718714001, -0.000514697647100001, 0.999620994692302 ; double yspace ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:step = -0.9765625 ; yspace:start = 146.850463958339 ; yspace:direction_cosines = -0.0186971433325, 0.999825193136882, -2.319984599e-08 ; double xspace ; xspace:comments = "X increases from patient left to right" ; xspace:step = 1.49999999999996 ; xspace:start = -95.4780255890689 ; xspace:direction_cosines = 0.999446254069973, 0.0186900576545041, 0.0275293837630133 ; short image(zspace, yspace, xspace) ; Any help would be much appreciated. thanks, mishkin

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left and right wm neighbors error
by Matt Colvin 14 Dec '07

14 Dec '07

Dear FreeSurfer folks, We recently had an error occur while processing two brains in recon2. We are using FreeSurfer version 4.0.1 for these subjects. The error message in both cases mentions that mri_fill could not find points where lh and rh wm were "nbrs" (I assume this is short for neighbors). Upon inspecting the aseg.mgz files for both brains, I found that, while there were one or two spots in each brain where lh and rh wm voxels did touch, it was much less than in other version 4.0.1 asegs that we have processed and inspected. In other words, there were plenty of places where the connection between the l and r wm was mediated by the corpus callosum label, but almost none where the wm were direct neighbors. Is there any way known for fixing this problem? Could it be related to the new corpus callosum label in the version 4 segmentation which was not present in earlier versions? Thanks in advance for any help anybody might be able to lend. Here is the end of the error message: #-------------------------------------------- #@# Fill Fri Dec 14 07:12:09 CST 2007 /disk/conte_raid1/freesurfer/Geller/02681/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.033 -0.026 0.146 -14.846; 0.010 1.114 0.190 -60.985; -0.140 -0.203 0.988 38.624; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.033 -0.026 0.146 -14.846; 0.010 1.114 0.190 -60.985; -0.140 -0.203 0.988 38.624; 0.000 0.000 0.000 1.000; reading segmented volume aseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs Linux eureka 2.6.9-22.0.2.ELsmp #1 SMP Thu Jan 5 17:13:01 EST 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Dec 14 07:12:31 CST 2007

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-noaparc flag
by Michael Harms 14 Dec '07

14 Dec '07

Hello, What is the role of the -noaparc flag in 'mris_make_surfaces' of FS v4? 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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