Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

grey/white matter volumes of cortical ROIs
by Jose Luis Cantero Lorente 02 Apr '09

02 Apr '09

Hi, I would like to obtain gray matter volume (not thickness) values for several new cortical ROIs that I have created with tkmedit, but to my knowledge this is not straight-forward with Freesurfer. We have tried this option: mris_anatomical_stats -l ?h.name.label <subject > Is that correct for my purpose? Could anybody tell me if there is another more correct way to aim this goal by using Freesurfer? How can I get the white matter volume values for the same ROIs? Any help would be very welcome. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Talairach
by Kelly Silva 02 Apr '09

02 Apr '09

Hello, If we have the brains well registered en relation to the Talairach (already checked with TKregister), is there any possibilty that the hemispheres of some subjects could be changed (left hemisphere as right and right as left) in the posterior statistical analysis? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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RES: [Freesurfer] Talairach
by Pedro Paulo de Magalhaes Oliveira Junior 02 Apr '09

02 Apr '09

You mean random swap? I doubt it. I would check the original data. Sent from my Nokia phone @E71 -----Msg original----- De: Kelly Silva Enviada: 02/04/2009 07:23:23 Assunto: [Freesurfer] Talairach Hello, If we have the brains well registered en relation to the Talairach (already checked with TKregister), is there any possibilty that the hemispheres of some subjects could be changed (left hemisphere as right and right as left) in the posterior statistical analysis? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Re: [Freesurfer] Measuring cortical thickness with high resolution data
by Nick Schmansky 02 Apr '09

02 Apr '09

Falk, Attached is a modified recon-all script where I've added a -hires switch to force the stream to not conform the data to 1mm^3, and to not use the atlases. Note that you should add the -clean flag to delete any work that had been done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz). However, in working with the .8mm data that you sent me, working with hires data will require quite a bit of manual intervention due to the fact that the atlases normally used cannot be used. The first problem occurs in skull-stripping, where quite a bit of dura and skull remains, and seems to have intensity values close to gray matter. This would have to be manually erased on each of the slices. If it is not erased (I did not do this because of the amount of time required), then the wm.mgz file, which is what is tessellated to create the initial surface, will be very wrong (it tessellates the garbage surrounding the gray matter). See also Bruce's prior posting on the problems of working with hires data in freesurfer. Nick On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote: > Hi Freesurfers, > > > > I’m trying to evaluate the usefulness of high resolution scans > acquired at 7T with an isometric voxel size of .6mm for the > measurement of cortical thickness. The inhomogeneities are taken care > of by dividing the scans with another scan of another sequence, so > they are not an issue anymore. > > > > My problem is that Freesurfer usually conforms the voxel size to 1mm > which is not desirable. I tried using the –cm and –noaseg flags for > the recon-all process to avoid the conformation and to skip the > subcortical segmentation, but another problem arises while using these > flags. > > > > The error I receive is occurring after the WM Segmentation and states > as follows: > > > > #-------------------------------------------- > > #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 > > > > cp wm.mgz wm.seg.mgz > > > > > > mri_segment -keep brain.mgz wm.seg.mgz > > > > preserving editing changes in output volume... > > doing initial intensity segmentation... > > using local statistics to label ambiguous voxels... > > computing class statistics for intensity windows... > > WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] > > GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] > > setting bottom of white matter range to 77.9 > > setting top of gray matter range to 89.4 > > doing initial intensity segmentation... > > using local statistics to label ambiguous voxels... > > using local geometry to label remaining ambiguous voxels... > > > > reclassifying voxels using Gaussian border classifier... > > > > removing voxels with positive offset direction... > > smoothing T1 volume with sigma = 0.250 > > removing 1-dimensional structures... > > thickening thin strands.... > > 20 segments, 4813 filled > > 10270 bright non-wm voxels segmented. > > 5589 diagonally connected voxels added... > > white matter segmentation took 2.4 minutes > > writing output to wm.seg.mgz... > > ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 > height=320. > > > > The dimensions of the data I’m trying to process is 320 x 320 x 224 > and is changed to 320 x 320 x 320 while using the –cm flag. It seems > the mri_segment process can’t handle any dimensions above 256 or I’m > missing another flag. > > > > Does someone has any ideas about that issue? > > > > Regards, > > Falk > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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LGI
by Gabriel Go.Es. 01 Apr '09

01 Apr '09

hi how can i compute the LGI and withe matter volume of my own ROIs? regards Gabriel _________________________________________________________________ ¿Quieres crear tus propios emoticonos gratis? Descubre cómo hacerlo en el Club Oficial de Messenger http://vivelive.com/ilovemessenger/

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Freesurfer installation: tksurfer not drawing
by dahlia＠nmr.mgh.harvard.edu 01 Apr '09

01 Apr '09

Hi, I've installed freesurfer on my Stanford linux machine, and while checking it can see subject bert in tkmedit. However, tksurfer isn't drawing in its window, and there's an error message surfer: ### redraw failed: no gl window open The installation is over Fedora Core 6 (build x86_64) How do I correct this? Thanks! Dahlia.

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Re: [Freesurfer] tksurfer error
by Pedro Paulo de Magalhães Oliveira Junior 01 Apr '09

01 Apr '09

I suggest you to migrate your virtual machine to VirtualBox: http://www.virtualbox.org/ Have you tried setting the autoredraw on in tksurfer interface? ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br 2009/4/1 Elisa Dell'Oglio <delloglio(a)bwh.harvard.edu> > I am indeed using a VMWare. I should probably check the VirtualBox version? > Or is there another fix that I could try? > Would you expect a different FPS (from glxgear)? > > Thank you very much for your time and patience. > > Elisa > > 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> It seems that you are using running this Centos inside a VMWare. >> TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in >> current vmware >> >> ----------------------------------------------------------- >> Pedro Paulo de M. Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> --- Novo Netfilter 3.0 www.netfilter.com.br >> >> >> >> 2009/4/1 Elisa Dell'Oglio <delloglio(a)bwh.harvard.edu> >> >>> Attached is the output of dmesg. I am not very familiar with evaluating >>> the output of glxgear. Here is a sample of the frames per second that is >>> printing: >>> >>> 7920 frames in 5.0 seconds = 1569.891 FPS >>> 8280 frames in 5.0 seconds = 1654.312 FPS >>> 7920 frames in 5.0 seconds = 1576.902 FPS >>> 8520 frames in 5.0 seconds = 1688.239 FPS >>> 9000 frames in 5.0 seconds = 1789.300 FPS >>> 8520 frames in 5.1 seconds = 1683.927 FPS >>> 8359 frames in 5.1 seconds = 1650.856 FPS >>> 8280 frames in 5.0 seconds = 1653.440 FPS >>> 8280 frames in 5.0 seconds = 1643.529 FPS >>> 8040 frames in 5.0 seconds = 1599.484 FPS >>> 9227 frames in 5.1 seconds = 1825.203 FPS >>> 8760 frames in 5.1 seconds = 1732.738 FPS >>> 8160 frames in 5.0 seconds = 1630.169 FPS >>> 8400 frames in 5.0 seconds = 1677.716 FPS >>> 8520 frames in 5.0 seconds = 1701.086 FPS >>> 8021 frames in 5.1 seconds = 1587.792 FPS >>> >>> thanks, >>> >>> Elisa >>> >>> >>> 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> >>> >>>> Try running glxgears >>>> >>>> Can you post the output of *dmesg *command >>>> >>>> >>>> >>>> 2009/4/1 Elisa Dell'Oglio <delloglio(a)bwh.harvard.edu> >>>> >>>> Thanks you. I actually tried this already (I saw this solution was >>>>> suggested to users that experienced the same problem). Unfortunately this is >>>>> not working, I still get the error message: >>>>> surfer: ### redraw failed: no gl window open >>>>> >>>>> Is there anything else that you would suggest to try? >>>>> >>>>> Thank you in advance, >>>>> Elisa >>>>> >>>>> 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior < >>>>> ppj(a)netfilter.com.br> >>>>> >>>>> If you are using tcsh >>>>>> >>>>>> setenv doublebufferflag 1 >>>>>> >>>>>> in bash >>>>>> >>>>>> export doublebufferflag=1 >>>>>> >>>>>> ----------------------------------------------------------- >>>>>> Pedro Paulo de M. Oliveira Junior >>>>>> Diretor de Operações >>>>>> Netfilter & SpeedComm Telecom >>>>>> --- Novo Netfilter 3.0 www.netfilter.com.br >>>>>> >>>>>> >>>>>> >>>>>> On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio < >>>>>> delloglio(a)bwh.harvard.edu> wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> I am running freesurfer on CentOS (5.2-x86_64). I get the folowing >>>>>>> error when I launch tksurfer: >>>>>>> surfer: ### redraw failed: no gl window open. >>>>>>> The result is that no surface is shown. >>>>>>> >>>>>>> Any advice on how to solve the problem? >>>>>>> >>>>>>> Thanks, >>>>>>> Elisa >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Elisa Dell'Oglio, MS >>>>> Research Associate to Dr. Bakshi >>>>> Brigham & Women's Hospital, Harvard Medical School >>>>> Laboratory for Neuroimaging Research >>>>> One Brookline Place, Suite 602 >>>>> Brookline, MA 02445, USA >>>>> Tel: 617-732-6977 >>>>> Fax: 617-732-6540 >>>>> Email: delloglio(a)bwh.harvard.edu >>>>> >>>> >>>> >>> >>> >>> -- >>> Elisa Dell'Oglio, MS >>> Research Associate to Dr. Bakshi >>> Brigham & Women's Hospital, Harvard Medical School >>> Laboratory for Neuroimaging Research >>> One Brookline Place, Suite 602 >>> Brookline, MA 02445, USA >>> Tel: 617-732-6977 >>> Fax: 617-732-6540 >>> Email: delloglio(a)bwh.harvard.edu >>> >> >> > > > -- > Elisa Dell'Oglio, MS > Research Associate to Dr. Bakshi > Brigham & Women's Hospital, Harvard Medical School > Laboratory for Neuroimaging Research > One Brookline Place, Suite 602 > Brookline, MA 02445, USA > Tel: 617-732-6977 > Fax: 617-732-6540 > Email: delloglio(a)bwh.harvard.edu >

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Sulcal depth and width
by Kelly Silva 01 Apr '09

01 Apr '09

Hello, How can I calculate the sulcal depth and the sulcal width for each hemisphere and for specific ROIs? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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grey/white matter volumes of cortical ROIs
by Jose Luis Cantero Lorente 01 Apr '09

01 Apr '09

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Re: [Freesurfer] tksurfer error
by Pedro Paulo de Magalhães Oliveira Junior 01 Apr '09

01 Apr '09

It seems that you are using running this Centos inside a VMWare. TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in current vmware ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br 2009/4/1 Elisa Dell'Oglio <delloglio(a)bwh.harvard.edu> > Attached is the output of dmesg. I am not very familiar with evaluating the > output of glxgear. Here is a sample of the frames per second that is > printing: > > 7920 frames in 5.0 seconds = 1569.891 FPS > 8280 frames in 5.0 seconds = 1654.312 FPS > 7920 frames in 5.0 seconds = 1576.902 FPS > 8520 frames in 5.0 seconds = 1688.239 FPS > 9000 frames in 5.0 seconds = 1789.300 FPS > 8520 frames in 5.1 seconds = 1683.927 FPS > 8359 frames in 5.1 seconds = 1650.856 FPS > 8280 frames in 5.0 seconds = 1653.440 FPS > 8280 frames in 5.0 seconds = 1643.529 FPS > 8040 frames in 5.0 seconds = 1599.484 FPS > 9227 frames in 5.1 seconds = 1825.203 FPS > 8760 frames in 5.1 seconds = 1732.738 FPS > 8160 frames in 5.0 seconds = 1630.169 FPS > 8400 frames in 5.0 seconds = 1677.716 FPS > 8520 frames in 5.0 seconds = 1701.086 FPS > 8021 frames in 5.1 seconds = 1587.792 FPS > > thanks, > > Elisa > > > 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> Try running glxgears >> >> Can you post the output of *dmesg *command >> >> >> >> 2009/4/1 Elisa Dell'Oglio <delloglio(a)bwh.harvard.edu> >> >> Thanks you. I actually tried this already (I saw this solution was >>> suggested to users that experienced the same problem). Unfortunately this is >>> not working, I still get the error message: >>> surfer: ### redraw failed: no gl window open >>> >>> Is there anything else that you would suggest to try? >>> >>> Thank you in advance, >>> Elisa >>> >>> 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> >>> >>> If you are using tcsh >>>> >>>> setenv doublebufferflag 1 >>>> >>>> in bash >>>> >>>> export doublebufferflag=1 >>>> >>>> ----------------------------------------------------------- >>>> Pedro Paulo de M. Oliveira Junior >>>> Diretor de Operações >>>> Netfilter & SpeedComm Telecom >>>> --- Novo Netfilter 3.0 www.netfilter.com.br >>>> >>>> >>>> >>>> On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio < >>>> delloglio(a)bwh.harvard.edu> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I am running freesurfer on CentOS (5.2-x86_64). I get the folowing >>>>> error when I launch tksurfer: >>>>> surfer: ### redraw failed: no gl window open. >>>>> The result is that no surface is shown. >>>>> >>>>> Any advice on how to solve the problem? >>>>> >>>>> Thanks, >>>>> Elisa >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> >>>> >>> >>> >>> -- >>> Elisa Dell'Oglio, MS >>> Research Associate to Dr. Bakshi >>> Brigham & Women's Hospital, Harvard Medical School >>> Laboratory for Neuroimaging Research >>> One Brookline Place, Suite 602 >>> Brookline, MA 02445, USA >>> Tel: 617-732-6977 >>> Fax: 617-732-6540 >>> Email: delloglio(a)bwh.harvard.edu >>> >> >> > > > -- > Elisa Dell'Oglio, MS > Research Associate to Dr. Bakshi > Brigham & Women's Hospital, Harvard Medical School > Laboratory for Neuroimaging Research > One Brookline Place, Suite 602 > Brookline, MA 02445, USA > Tel: 617-732-6977 > Fax: 617-732-6540 > Email: delloglio(a)bwh.harvard.edu >

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Freesurfer