Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

a question about mri_robust_template
by Guang Zeng 13 Apr '10

13 Apr '10

Hi, there, I have a question about mri_robust_template, I have a binary brainmask for each time point, I'd like to create a binary norm_template.mgz using mri_robust_template command. Has mri_robust_template an option to do nearest interpolation ? Thanks! Guang _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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skull strip error
by Dana W. Moore 13 Apr '10

13 Apr '10

Hi everyone, I am using freesurfer version 4.5.0, and have just gotten an error message that I have never received before. The end of the recon-all script is pasted below. what does this mean? #@# Skull Stripping Mon Apr 5 15:06:52 EDT 2010 /home/fs01/kab2003/FS/133_S_0525/mri mri_watershed -T1 T1.mgz brainmask.auto.mgz Mode: T1 normalized volume ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C *************************WATERSHED************************** Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 20676 Find the largest 110-component... heap usage = 128720 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 6553 voxels first estimation of the COG coord: x=124 y=177 z=184 r=110 first estimation of the main basin volume: 5673266 voxels mri_watershed Error: Problem with WM_MIN too small Linux compute-3-14.v4linux 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Apr 5 15:06:54 EDT 2010 Thanks, Dana

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mri_label2vol: how to make the opposite direction?
by John Gelburg 13 Apr '10

13 Apr '10

Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John

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Colortable in annotations
by Dankner, Nathan (NIH/NIMH) [F] 13 Apr '10

13 Apr '10

Hi all, I am running cluster corrections on data and attempting to display the resulting cluster maps. Is it possible to make all of the clusters in an annotation the same color? And if so, how? As it stands now, all of the clusters are given a different color. Thanks for your help, Nathan

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Job Announcement - Research Assistant in Brain Imaging
by Victoria Williams 13 Apr '10

13 Apr '10

Job Announcement: Research Assitant in Brain Imaging Boston, MA, USA Full time research assistant positions are available in structural and functional imaging of several clinical conditions including degenerative brain changes in individuals with neurological diseases, traumatic brain injury, and post-traumatic stress disorder using magnetic resonance imaging (MRI). The technician will be responsible for processing and analyzing MRI images, as well as for running analyses combining MRI data with neuropsychological, behavioral and other health associated data. The technician will also be trained in operation of the MRI scanner, and for maintaining and updating datasets. In addition, the research assistant will have the opportunity to take advantage of several educational opportunities, such as seminars and talks, in the Boston area. Candidates must have a high degree of computer literacy and be willing to learn to use our locally developed MRI analysis software. A long-term interest in neuroscience, neuropsychology, clinical psychology, or patient care is preferred, and a two-year commitment is required. Some knowledge of basic statistics is a plus. Applicants should send a resume and contact information for two references via email to David Salat: salat *at* nmr.mgh.harvard.edu with "RESEARCH ASSISTANT" as the subject line. More information about the Martinos Center can be found at http://www.nmr.mgh.harvard.edu/. Information about technical aspects of this work can be found at http://surfer.nmr.mgh.harvard.edu/fswiki.

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Scale factor for spherical distance
by Michael Waskom 13 Apr '10

13 Apr '10

Hi Bruce, I found some comments from your deep in the archive on converting distance measured on the sphere to distance on the folded surface: http://www.mail-archive.com/freesurfer@surfer.nmr.mgh.harvard.edu/msg00251.… Is this still the case? And, will loading the ?h.area file in matlab and summing the .vol vector give you total surface area, or is there a better way? Thanks! Mike

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volumetric version of fsaverage brain
by Ritobrato Datta 13 Apr '10

13 Apr '10

Hello All, Which is the volumetric version of the fsaverage brain in freesurfer ? Can you tell me what is it called ? Thanks Ri

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mri_surf2vol
by Jerald Zhao 13 Apr '10

13 Apr '10

Hi all, I'm a new user of freesurfer. It's a simple question. I want to convert ?h.smoothwm and ?h.smoothwm.nofix to .mgz as binary volume (foreground/background = 1/0). So I found mri_surf2vol command, but the command I used could be problem. > mri_surf2vol --template ./orig/001.mgz --volreg reg.dat --surface ../surf/lh.white --hemi lh error message is below. --- gdiagno = -1 ERROR: cannot recognize the type of ../surf/lh.white --- If mri_surf2vol cannot be used for what I want, is there any method to convert ?h.white? Thanks,

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Re: [Freesurfer] changing watershed threshold has no effect
by Andreas Berger 13 Apr '10

13 Apr '10

on one group of subjects i ran "recon-all -all -clean -wsthresh n", which according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags includes what "-clean-bm" does. on the other group i ran "recon-all -all -wshthresh n" after deleting everything and converting them from raw invol data to freesurfer format again. as i understand it, "-clean" is not required because no previous data is there to be overwritten/cleaned. to prevent confusion, i am not comparing these two groups, it's just that we have a separate group of subjects of which whe don't have the raw data, so i had to use -clean. i compared using "-wsthresh" against not using it in a few subjects from both groups. as far as the "-clean" flags are concerned, there is no bug: they do change the result, so i assume the previous volume is overwritten as it should, however the results are no improvement (see screenshots). On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) Allison Stevens <astevens(a)nmr.mgh.harvard.edu> wrote: > Andreas, > I'm not very clear on your response. Did using -clean-bm on the subjects > you had used -clean on when running with -wsthresh, change the skull strip > for the better? > > when you ran it on the already clean data set, you said using -wsthresh 0 > still did not get a good skull strip? > Allison > > -- > > On Fri, 9 Apr 2010, Andreas Berger wrote: > > > Sorry for the slow response, > > > > yes, the "-clean" flag should imply "-clean-bm" (among others) > > > > besides, on one group of the subjects i ran "recon-all -all -wsthresh n" after converting them from invol data again, everything from scratch (no cleaning required), with the same result. also, the fact that the surfaces did change (however not as i hoped) indicates that it's not a problem with the flags. > > > > > > > > > > On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) > > Allison Stevens <astevens(a)nmr.mgh.harvard.edu> wrote: > > > >> Andreas, > >> Did using -clean-bm work? > >> Allison > >> > >> -- > >> > >> On Mon, 29 Mar 2010, Allison Stevens wrote: > >> > >>> Andreas, > >>> Let me know how this turns out. The response you got about the command (using > >>> -clean-bm) is correct but since you used -clean, that should have worked just > >>> as well. Can you please let me know if using -clean-bm does anything > >>> differently from -clean? If so, we'll have to investigate this as a potential > >>> bug. > >>> Thanks, > >>> Allison > >>> > >>> > >> > >> > >> The information in this e-mail is intended only for the person to whom it is > >> addressed. If you believe this e-mail was sent to you in error and the e-mail > >> contains patient information, please contact the Partners Compliance HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was sent to you in error > >> but does not contain patient information, please contact the sender and properly > >> dispose of the e-mail. > >> > > > > > > -- Andreas Berger <andreas.berger.01(a)gmail.com>

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Extracting time series from aparc.a2009s+aseg.mgz
by liang wang 12 Apr '10

12 Apr '10

Hi FSusers, Is there a way to extract averaged BOLD signal from the identified cortical regions in aparc.a2009s+aseg.mgz. Thanks Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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