Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Inverse projection query
by Jason Connolly 18 Feb '11

18 Feb '11

Dear freesurfer experts: I have been using matlab to analyze a retinotopic dataset. However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface). Although the initial segmentations were done in freesurfer, my question is: Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface? If so, is the pipeline documented? Many thanks, Jason.

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Recon-all Error: _FindFacePath
by Jennifer Addicks 18 Feb '11

18 Feb '11

Hello, I have completed cortical reconstructions for 79 of 80 scans without error. However, the recon for one participant exited during topology correction with the following error message: ERROR: _FindFacePath: could not find path! Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Sun Nov 28 19:32:14 EST 2010 This error has been posted to the archive previously but the solution does not seem to accompany it. Any help would be appreciated. Thanks, Jennifer

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Re: [Freesurfer] error in test run
by Pom Sailasuta 18 Feb '11

18 Feb '11

Hello, I got errors below when testing my installation, I need help please. I had to donwload the centos4 version for my 32 bit desktop and there is no version for Fedora 14. [Pom@pom-PC freesurfer]$ recon-all -s bert -autorecon1 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20100808 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-r--r--. 1 Pom root 350150 Aug 10 2010 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux nu_correct: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /space/freesurfer/centos4.0_x86_64/stable thank you Pom On Thu, Feb 17, 2011 at 5:30 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Where did you get the 0.8 manual from? That must be 10 years old by now. > But to answer your question, we have an entire wiki dedicated to > documentation at surfer.nmr.mgh.harvard.edu/fswiki > > doug > Pom Sailasuta wrote: > >> Is there a later FreeSurfer manual other than version 0.8? >> >> The instruction in this version called file that does not exist >> (FreeSurferDefs.csh). >> >> >> -- >> Pom >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > -- Pom

1 0

glmfit-sim question
by Gabriel Go.Es. 18 Feb '11

18 Feb '11

Hello FreeSurfers I'm running some permutation tests and this induce me to a question, I'm using mri_glmfit-sim as recommended with the mc-z method, running 1000 permutations and seeding randomly, I have ran this with the same data two different times, and the results are bit different, could affect the number chossen for the seed flag affecting the results, what this seeding flag does in the command? Can any one point me to this? Bests, Gabriel

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very high/low values in the mri_glmfit results
by Joonkoo Park 18 Feb '11

18 Feb '11

Hi FreeSurfers, I'm running a group-level analysis of the fMRI data (beta-maps of individual subjects normalized onto fsaverage). One example would be like: mri_glmfit --y grouprfx/lh.con_0001.norm.mgh --surf fsaverage lh \ --glmdir grouprfx/lh.con_0001.osgm --osgm I understand that this is simply performing a one-sample t-test on each vertex. However, the resulting image (lh.con_0001.osgm/osgm/sig.mgh) contains some values that are extremely high or low (1e11 or 1e-11). I guess this is a representation of Inf and -Inf, but this is strange because when I run one-sample t-test manually in Matlab, the resulting t-values should be within an interpretable range. I have many subjects (close to 250), but I don't think that should be the reason. Any clues on why this is happening and how to resolve it? Thanks in advance as always! Joon

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Announcement: The 2011 FSL & FreeSurfer Course
by Bruce Fischl 18 Feb '11

18 Feb '11

We are pleased to announce the 2011 FSL & FreeSurfer Course, to be held in Montreal, Canada. It will run immediately before the Human Brain Mapping conference, which will be in Quebec City, a short plane/train/road journey from Montreal. The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to analyse their own FMRI and MRI data sets. The course lasts 5 days, from June 20-24. Numbers of attendees are strictly limited and are available on a first-come-first-served basis. For full information and to register for the course, please go to: http://www.fmrib.ox.ac.uk/fslcourse/montreal2011.html Regards, course organisers. --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------

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VBM in SPM and FreeSurfer
by soft.join Huang 18 Feb '11

18 Feb '11

Hi, FreeSurfer and VBM experts I'm a newer in the field, and not sure if this question is relevant to the list - any help will be appreciated. I am wondering about the difference between the data of FS and that of VBM in SPM. After searching in Google, I find a topic following, url: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-May/007710.html, and have some different opinions. In the discussion in above link, all believe that FS and VBM could give the same measurement - volume, yet I don't think so. I admit that we could get the volume of specific ROI by multiplying the thickness by the surface area, but through VBM in SPM, we get the mass( something like it) of the gray matter( multiply the density of gray matter by the volume). They have different meaning, to the best of my knowledge. I don't know if I get the right understanding. Thanks a lot in advance. Lijie Huang email: huanglijie.seal(a)gmail.com State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing China

2 1

manual
by Pom Sailasuta 17 Feb '11

17 Feb '11

Is there a later FreeSurfer manual other than version 0.8? The instruction in this version called file that does not exist (FreeSurferDefs.csh). -- Pom

2 1

skullstrip manual editing with tkmedit: will 5.0 results be compatible with 5.1?
by Hyunwoo Lee 17 Feb '11

17 Feb '11

Hello, I see that the new 5.1 version may be available soon. Thererfore, I was wondering if the brainmask.mgz file that contains the manual editing (using tkmedit from FS 5.0) will be compatible with the forthcoming FS 5.1 version. I am planning to use the 5.1 version for the longitudinal processing, and as the manual editing requires significant amount of time, I don't think it would be wise to do the manual editing with the 5.0 version if it is not going to be compatible. Thank you very much, and I look forward to hearing from you. Hyunwoo Lee

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retrieving persistent edits from manually edited reruns
by Binod Thapa-Chhetry 17 Feb '11

17 Feb '11

Hi, We are trying to set up a freesurfer pipeline to measure cortical thickness for a multisite project. I came across the show-edits option in freesurfer 5.0.0. My understanding from herehttp://surfer.nmr.mgh.harvard.edu/fswiki/Edits is that running show-edits is supposed to give a edits.mgz file with regions where user intervention has been performed. I am not able to figure out why edits.mgz for a freesurfer output without any user intervention is still showing some regions(on the brain's edge approximately). Also, edits.mgz for a freesurfer output with user intervention, is able to show edited brain regions(great!!) with the unexpected persistent regions close to what were present in unedited freesurfer output. I am not sure if I am using/interpreting things the right way. Any suggestion on this will be highly appreciated. Thanks, Binod Molecular Imaging and Neuropathology Division Department of Psychiatry, Columbia University New York, NY (212)543-5659

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