Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Anonymous svn checkouts?
by James Kyle 22 Feb '07

22 Feb '07

The freesurfer source is a fairly large download. I was hoping to keep our local copies up to date using an incremental update method like rsync or, ideally, a versioning system like svn. Forgive me if I've missed this information on the wiki. James A. Kyle UCLA Center for Cognitive Neuro Science David Geffen School of Medicine

2 1

strange overlay of averages
by Joongnam Yang 21 Feb '07

21 Feb '07

Hi all, I have a functional average (using FSL group analysis) and an anatomical average (using Freesurfer make_average_subject) across 6 subjects. (The functional average shows strong activation patterns in FSL ouput, report.html) However, when I overlay the averages, the expected functional activation was almost negligible. Would someone please suggest where I start tackling the problem? Thanks. Nam.

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Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 21 Feb '07

21 Feb '07

Thanks a lot Nick. I'll try to convert the AFNI skull strip into brainmask and nu and see if I can resume the pipeline. I put in the new values for the xfm and ran recon-all again with the notalairach flag. recon-all -s Nl-TAl-001 -notalairach -all However, it still quits at the watershed step. I ran another brain where the raw images were dcm and it ran fine so the problem is definitely something specific to this brain. Nick, I know that autorecon1 ran fine for you so I really have no clue why my machine quits at the watershed step even with the transform you gave me. Any clues, suggestions? Thanks a lot, Anil. On 2/14/07, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Anil, > > Here is the transform (the contents of the talairach.xfm file) that I > generated: > > Transform_Type = Linear; > Linear_Transform = > 9.265516e-01 5.678305e-04 2.317888e-03 3.736965e-01 > -8.173273e-04 8.513330e-01 8.824052e-02 -1.653205e+01 > -2.688466e-03 -1.064786e-01 9.460568e-01 1.780552e+01 ; > > Remember to use the -notalairach flag with recon-all when you create the > new talairach.xfm file, so that it doesnt get overwritten. > > 4GB is plenty to run Freesurfer, so it is strange that mri_watershed is > encountering out-of-memory errors. > > Nick > > > On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote: > > Also, I ran it on a Red Hat system and I'm still getting the error so > > I don't think it is a machine specific problem. Any suggestions. > > > > Thanks. > > Anil. > > > > On 2/14/07, Anil Roy <aroy85(a)gmail.com> wrote: > > Here are the details of the acquisitions: > > > > Images acquired on a 3T Signa scanner with a standard GE head > > coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm > > thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * > > 192 matrix) > > > > The machine has 4 gigs of RAM. Also, AFNI is able to talairach > > and skull strip. Is there a way I can input the files from > > AFNI to Freesurfer to resume the recon-all pipeline. > > > > Nick, is there a way for me to see your reg so that I can be > > sure that its not my created xfm that is causing this > > problem. > > > > Thanks, > > > > Anil. > > > > > > On 2/14/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > why is the background so high? Also, what field > > strength was this at? There > > looks to be dielectric-like center brightening. The > > contrast isn't terrible > > though. > > > > On Wed, 14 Feb 2007, Nick > > Schmansky wrote: > > > > > Bruce, > > > > > > the orig.mgz can be downloaded via the filedrop, see > > link in email > > > below. > > > > > > or i have copied it to: > > > > > > > /autofs/space/minerva_001/users/nicks/subjects/anil/mri > > > > > > N. > > > > > > > > > On Wed, 2007-02-14 at 17:02 -0500, Bruce Fischl > > wrote: > > >> put the .mgz somewhere and I'll take a look. And > > make sure it's the > > >> orig.mgz, which is un-normalized > > >> > > >> > > >> On Wed, 14 Feb 2007, Nick Schmansky wrote: > > >> > > >>> Anil, > > >>> > > >>> The image has almost no contrast. I've attached a > > TIFF of one slice. > > >>> How was this acquired? Bruce, any idea why it > > would be so white? > > >>> > > >>> Nick > > >>> > > >>> > > >>> On Wed, 2007-02-14 at 16:10 -0500, > > aroy85(a)gmail.com wrote: > > >>>> The following files have been uploaded to the > > Martinos Center FileDrop site > > >>>> by Anil Roy for you to download: > > >>>> > > >>>> (1) orig.mgz > > >>>> > > >>>> > > >>>> > > >>>> These files will expire in 30 days. > > >>>> > > >>>> To view or download these files, go in your web > > browser to: > > >>>> > > >>>> > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc… > > >>>> > > >>>> DO NOT SHARE this web address with anyone > > else. It is your personal access key to the files. > > >>>> > > >>>> Overall Comment about files from Anil Roy: > > >>>> > > >>>> Hi, > > >>>> > > >>>> Attached is the orig.mgz file for the subject > > that quits at the watershed step. > > >>>> > > >>>> Thanks, > > >>>> > > >>>> Anil. > > >>>> > > >>>> > > >>> > > >> > > >> > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Reprocessing the data with new FS release
by Gallo, Antonio (NIH/NINDS) [F] 21 Feb '07

21 Feb '07

Hi all, Since we have updated Freesurfer with the last (3.0.5) release, we were wondering at which point we should reprocess (i.e autorecon1, autorecon2, etc) our data in order to retain the edits we have made using the previous version. Thank you, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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question about surface-EEG fusion
by abel cruz vadell 20 Feb '07

20 Feb '07

Hello I need to import a file with the coordinates of the EEG electrodes (*.elc) obtained in the system POLHEMUS FASTRAK into the FreeSurfer system. Could I do that with the current version? Thanks in advance abel ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

2 1

Installing Freesurfer on Ubuntu 6.10 with AMD64 architecture
by Vincent Costa 20 Feb '07

20 Feb '07

Hi, I am attempting to install Freesurfer on a system running Ubuntu 6.10 with x86_64 architecture. On the Freesurfer Wiki it states that Debian users should install the Red Hat 9 package. I went ahead and did this, setting up and configuring Freesurfer following the directions listed on the Wiki. When I enter the tcsh shell I get the following output as expected: % tcsh -------- freesurfer-Linux-rh9-stable-pub-v3.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/vdcosta/freesurfer FSFAST_HOME /home/vdcosta/freesurfer/fsfast SUBJECTS_DIR /home/vdcosta/freesurfer/subjects MNI_DIR /home/vdcosta/freesurfer/mni GSL_DIR /home/vdcosta/freesurfer/lib/gsl FSL_DIR /home/vdcosta/freesurfer/fsl However when I attempt to test my install, all commands result in the following error: /home/vdcosta/freesurfer/bin/tkmedit.bin: Command not found. tkmedit can be replaced by other commands to generate the same error message. If I enter on the command line: recon-all --help | less : the returned ouput is what appears to be a full manual on all Freesurfer processing steps. Do I need to install the x86_64 package? The following is my .tcshrc file: setenv AFNI_PATH ~/afni set path = ($path .) set path = ($path $AFNI_PATH .) set path = ($path ~/bin) set history = 100 alias copy cp alias del rm alias dir ls alias find 'find . -name \!^ -print' alias dir/p 'ls . | more' alias type 'cat \!^ | more' alias xterm 'xterm -sb &' alias h history alias m more= setenv FREESURFER_HOME /home/vdcosta/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Any help in getting Freesurfer running would be greatly appreciated. Thanks, Vinny Costa vdcosta at ufl dot edu

4 6

reg-feat2anat problem
by Elaine Leung 20 Feb '07

20 Feb '07

Hello, I'm trying to display some FEAT statistics on a surface I created using Freesurfer using instructions from http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html. The automatic registration function reg-feat2anat seems to have failed and I'm not sure what I should do to re-orient the slices better. I've attached a picture, hopefully it will convey my problem. Also, looking at the log files, I noticed the line INFO: could not find /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file Where do I get the file avg152T1_brain.mat? Thanks for your help, Elaine

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Getting started with tutorial data.
by McLean John (NHS Greater Glasgow & Clyde) 20 Feb '07

20 Feb '07

Hi, I am new to Freesurfer and i'm hoping to learn how to use it by working through the tutorial data. I have installed FS correctly and ran recon-all -s bert -autorecon1 This completed without any errors. When i downloded the tutorial data: (buckner_data-tutorial_subjs.tar.gz) i noticed the file was only 2Gb (compressed), rather than the 6.5Gb reported in the FS documentation. After unzipping the files i am now concerned i do not have the full dataset that was intended. Within the folder .../buckner_data/tutorial_subjs i only seem to have the following folders and files bert fbert.feat group_analysis_tutorial fbert.design.fsf fbert.nii.gz I do not seem to have a folder called scrips, which i think i should have? Can anyone tell me where i am going wrong. I tried to start working through the FS tutorials and i failed at the first hurdle. Any help or comments are much appreciated. Best wishes John ********************************************************************** Information in this message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies; please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

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problem in running recon-all
by Shahabuddin Ansari 20 Feb '07

20 Feb '07

Hi, I ran "recon-all -subjid 2144 -all" and it just got frozen after a while. I have attached the log herewith. Appreciate your help. Thanks! Shahab --------------------------------- Need a quick answer? Get one in minutes from people who know. Ask your question on Yahoo! Answers.

2 1

volumes of aseg, aparc
by Woo Suk, Tae 20 Feb '07

20 Feb '07

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear Freesurfer experts. Are the volumes of aseg, aparc files absolute volumes measured in native space or measured after spatial normalization? Woo Suk, Tae Seoul, Korea

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