Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

installation problem in ubuntu
by Liukarl 21 Feb '11

21 Feb '11

Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” -------- freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid <subjid> -<process directive>…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! Jie

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segment lobes
by Adil Javed 19 Feb '11

19 Feb '11

Hi, This may be complicated, but ... I would like to segment various brain lobes, save them as mask files, convert them to NIFTI format, feed them to FSL for tractography. Can anyone tell me if it is possible to segment brain lobes in freesurfer and then feed them to fsl? many thanks in advance, AJ

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Help ! Error for generating *.mgz files
by xiaotian yin 19 Feb '11

19 Feb '11

Hi, Thank you for reading this email ! I am a newbie to Medical Imaging, and am learning to use FreeSurfer for surface construction. Already installed FreeSurfer in Ubuntu, and the installation has been verified to be 100% successful. I got a bunch of data (coming in pairs of *.hdr and *.img), and I am trying to convert them to *.mgz files, so that I can use recon-all then. but when I call mri_convert as follows: mri_convert Rcing.img Rcing.mgz I got the following error : mri_convert Rcing.img Rcing.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from Rcing.img... ----------------------------------------------------------------- INFO: could not find /mnt/Data/Rcing.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: -40, . INFO: if not valid, please provide the information in /mnt/Data/Rcing.mat file ----------------------------------------------------------------- Segmentation fault I have searched the freesurfer website ... no luck .... Would you mind to give me some advice or hints ? Thank you so much ! Best Tim

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vertex coordinates: tksurfer vs sig.cluster.summary
by Marco Loggia, PhD 19 Feb '11

19 Feb '11

Dear Freesurfers, I have noticed a slight incongruity between the coordinates outputted by sig.cluster.summary and those in tksurfer. For instance, in the .summary file one of my maxima (VtxMax=92221) has the following "Tal" coordinates: -14.9, -62.2, 57.5. Now, if I open the fsaverage with tksurfer, and I enter 92221 as my Vertex Index, the Vertex Talairach coordinates are slightly different than those reported by the .summary file (-14.89, -61.61, 57.01). Is this because the Max in my significant cluster actually spans multiple adjacent vertices, and therefore the coordinates provided by the .summary file represent an average across those vertices? As for the "MNI Talairach", my understanding is that these are from the MNI305, right? If so, why the "Talairach" part of the name? Thanks, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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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

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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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