Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

aseg.auto.mgz
by Tom Bayer 13 Apr '06

13 Apr '06

I'm having problems with the output of recon-all -autorecon2. proceeding down the recon-all dev table, I checked the outputs of each step. everything looks good until aseg.auto.mgz everything after has problems. What kind of manual intervention do I need to do for this? -Tom

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Manual intervention for skull stripping
by Lee HL 13 Apr '06

13 Apr '06

Hi, I'm a freesurfer newbie. I was following the instructions from the beginners guide to fix bad output from skull stripping. However, it didn't work as it should be as described below (see italics) when I clicked on my middle button. Is there any option that I could do to re-assign my buttons to perform the operation? Thank you very much for your help! "Use Ctrl-1 and Ctrl-2 to cycle between the two volumes. Find a place in the image where the cerebellum is missing in the output volume, then use the middle button on the mouse to paint in cerebellum from the auxiliary volume. Cycle back and forth between the volumes frequently so you know where you are." -- extracted from the internet source. -- Best wishes, HweeLing Research Scientist Cognitive Neuroscience Laboratory Singapore Health Services

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yakview ttrouble
by Sebastian Moeller 13 Apr '06

13 Apr '06

Dear freesurfers, ran into troubles with yakview (centos4_x86_64-3.0.1-pub-full under Suse 9.3 x86_64) the -nosplash option in line 398 of fsfast/bin/yakview causes a "Warning: Type-ahead buffer overflow." from the installed matlab 7.1 and, not completely unexpected, some corruption. The corruption I observed was a wrong TR and a way off scaling of the colorbar, BTW. Anyway, putting a hash before the -nosplash helps (with the caveat that the splash window opens, albeit transiently). I still see other issues with my install of yakview.m, like the help window (and any other msgbox) gets a copy of the statusline written over line 7. It seems like set_text() gets periodically called with 'gca' as argument, a bit b0rked, if set_text(gca, ud) is called while the help window is active, as gca now points to this window. A Q&D cure is to secure the two call to se_text(gca,ud), with the following construct: if (gcf == ud.hThisYakFig), set_text(gca,ud); end Oh yeah zooming does not really work, but I did not investigate further One more thing though, what to use -v1 or -v2? Ahoi & thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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RE: [Freesurfer] FW: FW: Recon-all longitudinal script
by Nguyen, Thang Q 12 Apr '06

12 Apr '06

Hi Jenni, Yes I have tried it. I guess I should have been clearer when I wrote "I have added the mgz extension", my mistake. Thanks, -Thang -----Original Message----- From: Jenni Pacheco [mailto:jpacheco@nmr.mgh.harvard.edu] Sent: Wednesday, April 12, 2006 3:13 PM To: Nguyen, Thang Q Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: Recon-all longitudinal script Hi Thang, I'm not sure if you've tried this, but try adding -mgz to the command line when running recon-all-nmr-long. Jenni On Wed, 12 Apr 2006, Nguyen, Thang Q wrote: > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Tuesday, April 11, 2006 5:42 PM > To: Nguyen, Thang Q > Subject: Re: FW: Recon-all longitudinal script > > Hi Thang, > > please post this to the list > > Bruce > On Tue, 11 Apr 2006, Nguyen, Thang Q wrote: > >> Hello Bruce Fischl, >> I was wondering if you could help me with this Freesurfer issue. I am >> trying to run the longituduinal script (recon-all-nmr-long) that Xiao >> sent me. We have installed the latest 2006 version of Freesurfer > which >> works in mgz format. I have tried running recon-all on one subject > and >> running the longitudinal script on the second subject. Unfortunately, >> it errors out saying that the script can't find the mgz format. I > have >> added the mgz extension and it also gives me the same problem. >> I have tried recon-all on the second subject as well and then running >> the longitudinal script but it gives me this error: >> >> ***************************************************** >> Sphere rh Mon Apr 10 18:04:19 PDT 2006 >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR2/scripts >> cp >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR/surf/rh.sphere >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR2/surf/rh.sphere >> --------------------------------------------- >> Surf Reg rh Mon Apr 10 18:04:19 PDT 2006 >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR2/scripts >> Too many )'s. >> >> ***************************************************** >> Since Xiao left, I no longer have a contact for this problem. I have >> contacted Karl Helmer and he hasn't responded. I was wondering if you >> could help me. Thank you, >> Thang Nguyen >> >> >> ________________________________ >> >> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Friday, April 07, 2006 3:36 PM >> To: Nguyen, Thang Q >> Subject: Re: Recon-all longitudinal script >> >> >> I think you run recon-all on the first time point, then -long on the >> subsequent ones. But I've never actually run it myself :). >> >> doug >> >> >> >> >> Nguyen, Thang Q wrote: >> Hello Doug Greve, >> I am trying to run a longitudinal analysis using the > recon-all-nmr-long >> binary from Xiao. I was wondering if you could answer some questions > I >> have. Do I need to process each longitudinal scan using recon-all > first >> and then apply the longitudinal analysis to the first scan or can I >> simply run the recon-all-nmr-long for the subsequent subjects without >> running recon-all on those datasets? >> Thank you for your time, >> -Thang >> >> >> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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FW: FW: Recon-all longitudinal script
by Nguyen, Thang Q 12 Apr '06

12 Apr '06

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, April 11, 2006 5:42 PM To: Nguyen, Thang Q Subject: Re: FW: Recon-all longitudinal script Hi Thang, please post this to the list Bruce On Tue, 11 Apr 2006, Nguyen, Thang Q wrote: > Hello Bruce Fischl, > I was wondering if you could help me with this Freesurfer issue. I am > trying to run the longituduinal script (recon-all-nmr-long) that Xiao > sent me. We have installed the latest 2006 version of Freesurfer which > works in mgz format. I have tried running recon-all on one subject and > running the longitudinal script on the second subject. Unfortunately, > it errors out saying that the script can't find the mgz format. I have > added the mgz extension and it also gives me the same problem. > I have tried recon-all on the second subject as well and then running > the longitudinal script but it gives me this error: > > ***************************************************** > Sphere rh Mon Apr 10 18:04:19 PDT 2006 > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR2/scripts > cp > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR/surf/rh.sphere > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR2/surf/rh.sphere > --------------------------------------------- > Surf Reg rh Mon Apr 10 18:04:19 PDT 2006 > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR2/scripts > Too many )'s. > > ***************************************************** > Since Xiao left, I no longer have a contact for this problem. I have > contacted Karl Helmer and he hasn't responded. I was wondering if you > could help me. Thank you, > Thang Nguyen > > > ________________________________ > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Friday, April 07, 2006 3:36 PM > To: Nguyen, Thang Q > Subject: Re: Recon-all longitudinal script > > > I think you run recon-all on the first time point, then -long on the > subsequent ones. But I've never actually run it myself :). > > doug > > > > > Nguyen, Thang Q wrote: > Hello Doug Greve, > I am trying to run a longitudinal analysis using the recon-all-nmr-long > binary from Xiao. I was wondering if you could answer some questions I > have. Do I need to process each longitudinal scan using recon-all first > and then apply the longitudinal analysis to the first scan or can I > simply run the recon-all-nmr-long for the subsequent subjects without > running recon-all on those datasets? > Thank you for your time, > -Thang > > > > > >

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unpacking anonymized data
by Doug Greve 12 Apr '06

12 Apr '06

I just wanted to give people some warning about unpacking/converting anonymized Siemens dicom files. Siemens inserts some ascii information into their dicom files (what I call the "ascii header"). This is inserted into a "private" field in the dicom header. Some anonymizers will strip this information out of the dicom file. If the dicom file contains a mosiac (eg, as with functionals), then it will not be possible to unpack it using the tools in freesurfer if the ascii header is gone. If the dicom file contains individual slice images (non-mosaics), then it is possible to unpack it correctly even if their is no ascii header. There is currently a bug in mri_convert/unpacksdcmdir that might cause a slice reversal if the ascii header is not there. If you acquired data sagitally, this would mean a left-right flip. This bug has been fixed (live in dev and stable tomorrow). Even so, be very careful when anonymizing your data. You should do some sort of check against unanonymized data to assure that nothing funny has happened. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Gnome terminal do not support OpenGL GLX extensions with freesurfer
by jorge luis 12 Apr '06

12 Apr '06

Hello all I am just starting to use freesurfer in our new laboratory of functional neuroscience. I have a Dell machine with 64 bits Intel Dual Xeon processors. I have installed the 64 bits Linux Centos 4 Operating System. Also the machine has an nVidia Quadro FX 4500 graphic card. I have installed freesurfer for x86-64 Centos 4 successfully but when I run the command: tkmedit bert orig.mgz I got this message displayed in the prompt: freeglut (tkmedit): OpenGL GLX extension not supported by display ':0.0' I was using the GNOME 2.7.3 Terminal, Copyright © 2002 Havoc Pennington I will appreciate any help to overcome this problem In advance Thank you ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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color scale bar
by anthony gallo 11 Apr '06

11 Apr '06

if you are using the overlay color display how can you configure the scale? In the paper "Measuring the thickness of the human cerebral cortex from magnetic resonance images" the images show the overlay color bar in many different scales. Thanks

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Translating labels created from aseg to DTI bfloats
by Jonathan Wisco 11 Apr '06

11 Apr '06

Hi, is there a way to translate a label created from the aseg segmentations to DTI bfloat data? I know I asked this before, but can't find the answer in my e-mails. Thanks. -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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RE: [Freesurfer] Recommendation for Linux machine
by Durastanti, Valentina (NIH/NINDS) [F] 11 Apr '06

11 Apr '06

I used the old command (csurf) to open freesurfer and then I tried to open the volume from that! It works but don't show me the segmentation lines on the brain volume (even if it show the lines on the wm volume) thanks Valentina -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, April 11, 2006 2:21 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Chunchun Ni; Freesurfer Mailing List Subject: RE: [Freesurfer] Recommendation for Linux machine what is the command-line that was typed? On Tue, 2006-04-11 at 15:13 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > Dear Bruce, > I'm trying to open some images that I analyzed with the old version of > Freesurfer but when I charge the brain volume on tkmedit it doesn't show > me the red and green line! Have you any suggestion? > Thanks > Valentina > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Freesurfer