Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

Vertex values
by Oya, Hiroyuki 16 Jan '10

16 Jan '10

Dear Experts, Is it possible to import surface vertex index and corresponding values into Matlab? Thank you very much . Hiroyuki

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SPM-VBM and freesurfer
by Lena Palaniyappan 16 Jan '10

16 Jan '10

Hi all Not sure if this question is relevant to the list - any help will be appreciated. I have a t-statistics map from comparing 2 groups in VBM approach from SPM8 I want to apply this thresholded t map as a mask ROI to see thickness differences in the same groups using freesurfer. Is this possible? Will I be better off doing FSL_VBM instead - if that is easy to run with freesurfer? cheers Lena ________________________________________________________ Lena Palaniyappan PhD student| Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 1

skull stripping
by laura_dg80 16 Jan '10

16 Jan '10

Hi! I have some difficulties in the Skull stripping. I'm not experienced and I'm not able to evaluate if my job is good. I visualize the result with Tkmedit and I see that some skull often remain in the eye soked region . Could you send me some example of "GOOD" and "Bad" skull stripping of this region? Thank you Laura

2 1

retinotopic mapping stimuli
by Vadim Axel 16 Jan '10

16 Jan '10

Hi, I prepare to run retinotopic mapping experiment. I need only polar angles, since I am interested in localization of V1,V2 and V3 only. So, on inflated brain I plan to locate regions' reversals (vertical and horizontal meridians). For the moment, I plan to use FreSurfer for only inflating the brain (fMRI data I analyze in SPM). I have created two different stimuli and I would like to know: 1) Since I need only vertical and horizontal meridians is it OK to have only 90 degrees sector? 2) Since I need only vertical and horizontal meridians, how effective it would be instead of Fourier phase analysis to make a GLM with a boxcar function? 3) Should my sector start straight at meridian line (as I did), or the sector should encompass it from both sides? 4) Is it optimal to make each sector block length about 10-12 secs The stimuli: http://www.youtube.com/watch?v=iW8sk44eyck http://www.youtube.com/watch?v=DcGZW1pM-28 Thanks a lot for your help, Vadim

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Incomplete skull striping but correct segmentation
by Estephan Moana 15 Jan '10

15 Jan '10

I had some subjects processed through the standard recon-all pipeline that had some remaining skull just below the frontal lobe (superior part of the orbit). The segmentation as checked in tkmedit appeared to be ok, i.e. it was not considering the skull parts as white matter. The reconstructed cortical surfaces also appeared to be good in tksurfer. Playing with the watershed value did not provide much improvement, and I assume that to clean up the images adequately I would have to do so by hand. My question is: should I be concerned about improving skull stripping for these subjects, given the good segmentation and cortical reconstruction obtained? Thank you. Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Rm 2140 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 moana(a)email.unc.edu

1 0

Tiff images created by tksurfer
by Oya, Hiroyuki 14 Jan '10

14 Jan '10

Hello tksurfer can save multiple surface renderings of the brain as 600 x600 tiff formatted images. If anybody can tell me the relationship between center of the image and the brain, that would be appreciated. Thank you very much. Hiroyuki

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Recon-ALL error
by mmoayedi＠uhnres.utoronto.ca 14 Jan '10

14 Jan '10

Hi Everyone, Here is a newish error I've encountered- does anyone know how to fix it, or what it means? status file for recon-all: Thu Jan 14 19:48:44 EST 2010 #@# MotionCor Thu Jan 14 19:48:50 EST 2010 #@# Nu Intensity Correction Thu Jan 14 19:49:05 EST 2010 #@# Talairach Thu Jan 14 19:51:03 EST 2010 #@# Talairach Failure Detection Thu Jan 14 19:52:05 EST 2010 Linux 2.6.23.1-21.fc7 #1 SMP Thu Nov 1 21:09:24 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Jan 14 19:52:05 EST 2010 --------------------- recon-all.error: PWD /storage/AllUsers/Nathalie/FreeSurferData/Subjects/A1/a1/mri CMD talairach_afd -T 0.005 -xfm transforms/talairach.xfm --------------------- from command line: talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jan 14 19:52:05 EST 2010 /storage/AllUsers/Nathalie/FreeSurferData/Subjects/A1/a1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0001, pval=0.0000 < threshold=0.0050) Linux 2.6.23.1-21.fc7 #1 SMP Thu Nov 1 21:09:24 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Jan 14 19:52:05 EST 2010 -------------------------- As usual, any, and all help, is much appreciated!!! Massih

2 1

mri_convert questions?
by Brain Apprentice 14 Jan '10

14 Jan '10

Hello, I was just wondering if there was a way in mri_convert to conform a MRI scan so that the output file is 16-bit? The reason I ask is that I am trying to create dual pipelines. One pipe for Freesurfer and the other pipe for SPM and it would be nice to use mri_convert to generate the data for both from DICOM files. Thanks, BA

4 3

Keyboard problem in FreeSurfer
by XJ Kang 14 Jan '10

14 Jan '10

Hi, I am using FreeSurfer 4.5, on a 64-bit Dell Precision workstation. The OS is Centos 5.4. I cannot input anything in tkmedit using my keyboard. I can only input curvature file names in tksurfer, but not overlay file names and threshold values. I searched the mailing archives, same thing happened to Hiroyuki (See below). I am wondering if this is a problem for 64-bit machine. Any suggestions? Thank you. XJ Kang >Dear all, > >I am running freesurfer 4.5 on Ubuntu9.10(64bit). >Is anybody experiencing " lost keyboard " problem? >I cannot put any number in tkmedit and tksurfer using keyboard. > >Thank you. > >Hiroyuki

4 3

Re: [Freesurfer] poll question: Mac OS Tiger users
by Ed Gronenschild 14 Jan '10

14 Jan '10

Hi Nick, I'm using Freesurfer on different Macs, of which one with Tiger OS and ppc. So, I kindly ask you to continue support for Tiger OS and ppc for at least this year. Ed On 13 Jan 2010, at 23:14, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > for the Mac OS users out there: > > who still needs a Tiger OS build of freesurfer? and on what processor > (intel or ppc)? > > i'd like to discontinue support for Tiger (and redirect efforts toward > working with Snow Leopard), but if enough people still need the Tiger > build then we can keep our creaky-old machine around to do this. > > Nick

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Freesurfer January 2010