Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30078 discussions

Creating a Volume from the finished Pial Surface
by Cochrane Jamison 18 Mar '08

18 Mar '08

Hello. I am still very new to freesurfer. I have finished running a complete recon all process on one mri. I used a very good scan, which produced great results from freesurfer. However, I am having trouble producing some usable output. I want to create a volume from the finished pial surface so that I can load it into another program for dipole analysis. I have read through the archives and come across the command mri_surf2vol that seems to be able to do what I am trying to do. I am having problems with is though. Here is where I started: MEG-PC:~/freesurfer/subjects/C0668_Duck/mri> mri_surf2vol --hemi lh --template ../orig/001.mgz --outvol left_filled_pial.img --fillribbon --surf pial gdiagno = -1 A surface value path must be supplied In another post, I saw where the user had used the lh.thickness for the surface values, so I tried the same and got this: MEG-PC:~/freesurfer/subjects/C0668_Duck/mri> mri_surf2vol --hemi lh --surfval ../surf/lh.thickness --template ../orig/001.mgz --outvol left_filled_pial.img --fillribbon --surf pial gdiagno = -1 A volume registration file must be supplied I have read the help file about tksurfer2 and creating a volume registration file, but I cannot exactly figure out what all I need for inputs, and what kind of output I want exactly. I know this may not be as much detail as you need, so please let me know if you have any questions. Thank you for the help. William

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qdec display problem
by Michael Harms 18 Mar '08

18 Mar '08

Hello, Has anyone reported, or have you experienced, the following issue with the qdec surface display: As soon as I left click on the surface (as if to rotate it), the display seems to get "confused" about how to render the surface properly -- see attached jpeg for a visual. If I select an alternative surface among 'inflated', 'pial', or 'white', the surface is temporarily displayed correctly until I left click on it again. I'm using FS v4.0.2 from the 32-bit CentOS build. 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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Longitudinal analysis
by Wayne Su 18 Mar '08

18 Mar '08

I have a couple of scans which were failed during mri_cc (corpus callosum segmentation). Log file is attached here. #@# CC Seg Mon Mar 17 11:21:32 PDT 2008 \n mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz ERP_3000_Month1L \n reading input aseg from aseg.auto.mgz writing aseg with cc labels to aseg.auto_CCseg.mgz mri_cc: volume /Applications/freesurfer/subjects/ERP_3000_Month1L/mri/aseg.auto.mgz already has CC in it reading aseg from /Applications/freesurfer/subjects/ERP_3000_Month1L/mri/aseg.auto.mgz Darwin centaurs.vchri.med.ubc.ca 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 recon-all exited with ERRORS at Mon Mar 17 11:21:35 PDT 2008 I am using version 4.0.1. Could anyone point out what's the problem? Thanks. Wayne

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tksurfer - viewer and tktool screen freeze
by Carline van der Pol 18 Mar '08

18 Mar '08

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Re: [Freesurfer] Invisible flattened cortex
by SHRIKANTH KULASHEKHAR 18 Mar '08

18 Mar '08

Hi Bruce, I had earlier written to you with a problem visualizing the flattened lateral section of the cortex, while the flattened medial section was OK. I tried the flattening process on another subject's cortex. This time I could visualise the lateral section but not the medial section. Again the flattening processes were accompanied with no errors. For the flattening parameters were Medial: mris_flatten -w 0 size 20 Lateral: mris_flatten -w 0 size 12 I am working on Fedora core 8 using Freesurfer version v4.0.2. Any idea on what could be wrong ? Thank you shriks ----- Original Message ---- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: SHRIKANTH KULASHEKHAR <contactshriks(a)yahoo.co.in> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, 14 March, 2008 3:21:29 PM Subject: Re: [Freesurfer] Invisible flattened cortex what machine type/os are you working on? On Fri, 14 Mar 2008, SHRIKANTH KULASHEKHAR wrote: > Hi Bruce, > > This problem is in spite of rotating it. I am sorry I did not mention this in my earlier post. > > shriks > > ----- Original Message ---- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: SHRIKANTH KULASHEKHAR <contactshriks(a)yahoo.co.in> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Friday, 14 March, 2008 3:16:19 PM > Subject: Re: [Freesurfer] Invisible flattened cortex > > Hi Shriks, > > try rotating it. > > Bruce > On Fri, 14 Mar 2008, SHRIKANTH KULASHEKHAR wrote: > >> Hi, >> >> I am trying to flatten the lateral and medial sections of the brain. The flattening processes using >> mris_flatten -w 0 12 work fine without any errors. And I am able to visualize the flattened medial portion. However, when I load the flattened lateral portion the window is blank with no errors. I can visualize the patch created for the lateral section though. >> >> Any ideas on what could be wrong ? >> >> Thank you, >> Shriks >> >> >> >> >> Forgot the famous last words? Access your message archive online at http://in.messenger.yahoo.com/webmessengerpromo.php > > > > > > > Why delete messages? Unlimited storage is just a click away. Go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Bollywood, fun, friendship, sports and more. You name it, we have it on http://in.promos.yahoo.com/groups

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tksurfer overlay scale bar color
by Scott 17 Mar '08

17 Mar '08

Hi, Is there a way to change the text color of the overlay scale bar labels in tksurfer? I see them as black text on a black background - completely unreadable unless i move the brain under the scale bar. Thanks, Scott

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CO-DIRECTOR: SAN FRANCISCO BAY AREA MRI CENTER
by David L Woods 17 Mar '08

17 Mar '08

The Human Cognitive Neurophysiology Laboratory (affiliated with UC Davis and the VA Northern California and located in the San Francisco Bay Area) is searching for a co-director to assist in directing ongoing VA-sponsored research programs using structural and functional MRI. Research programs include the development of quantitative automated lesion detection techniques to evaluate traumatic brain injury, longitudinal investigations of neuroplastic changes associated with neurological recovery and cognitive/perceptual training and fMRI studies of auditory and visual selective attention (see www.ebire.org/hcnlab <http://www.ebire.org/hcnlab> for further details). This is a full-time research position at the equivalent of Assistant or Associate Professor Level with up to three years of salary and research support deriving from existing research grants. The applicant is expected to develop successful independent research programs during the 3-yr period. Post-doctoral training, evidence of research productivity, and prior grant funding are highly desirable. The applicant should have a strong background in MRI/fMRI or other brain imaging techniques (e.g., PET, TMS, MEG, EEG, etc.). Resources include a Philips Eclipse 1.5T scanner (to be upgraded to 3T in 2009), Bio-semi EEG and ERP recording systems, Magstim TMS stimulators, SR eye tracking systems, and multiple testing rooms for physiological, psychophysical and behavioral experiments. Opportunities exist for UC faculty appointment and collaborations with scientists at UC Davis and UC Berkeley. US citizenship is preferred. Salary: $70,000-$100,000 depending on experience. Interested candidates should email a statement of research interests, C.V., list of research grants and postdoctoral fellowships, representative publications, and the names of three references to dlwoods(a)ucdavis.edu. Applications will be accepted until the position is filled. -- David L. Woods, Professor of Neurology, Dept. of Neurology,UC Davis, Chief, Clinical Neurophysiology and Chief, Research MRI, Neurology Service (127E), Bldg. R4, VANCHCS, 150 Muir Rd., Martinez, CA 94553 Tel (925) 372-2571, Fax (925) 229-2315 Email:dlwoods@ucdavis.edu Website: http://www.ebire.org/hcnlab

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glmfit/qdec
by Hoppmann, Fee 17 Mar '08

17 Mar '08

Dear all, I ran an analysis on some old data using qdec. Surprisingly, I discovered that the significant areas now look differently than when computed using glmfit. I reran the analysis with qdec and glmfit, but the results are still different, although the underlying question is reduced to minimum (is there a difference between two groups), fwmh is 10 for both, threshold is the same, the exactly same subjects are used... How is that possible? Thanks for help, Fee Hoppmann

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spmregister-sess vs. autoreg-sess
by Tsung-Ren Huang 17 Mar '08

17 Mar '08

Dear Freesurfers, There seems to be two ways for functional/structural registration. One is spmregister-sess, and the other is autoreg-sess. What are the differences between these two scripts? Which one do you prefer to use and why? Thanks! Tren

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license file for FS upgrades
by Mischka Gerken 15 Mar '08

15 Mar '08

Hello, I am trying to upgrade my FreeSurfer from 4.0.1 to 4.0.2 in order to trouble shoot some qdec issues. I am having difficulty getting freesurfer to recognize my .license file. Does one need to get a new liscence when upgrading versions? I am running Mac OS tiger on a PowerPC. -Mischka.

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