Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

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by Ning Liu 10 Aug '07

10 Aug '07

I copied some subjects' data to my computer, but i cannot run the surfer here is the command line: tksurfer MGH_Ruphert lh inflated screen output surfer: current subjects dir: /Users/lning/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/lning/subjects/MGH_Ruphert surfer: ### Could not find anatomical header information -- When was the last time you had a conversation with the moon or made a wish on a falling star? The time is now.

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free surfer download issues
by Jeffrey Dutschke 09 Aug '07

09 Aug '07

Hi all, I have tried several times to download the free surfer software, and have thus far failed to do so because the download stalls at around 800mB into the file download. Are you able to advise as to how I might overcome this problem. Specifically I have tried to download both the Apple intel i686 and tiger file. I have been unsuccessful in attempts to download it using a web-browser, a ftp client, and through the terminal command line. I hope to be able to use the software to generate the surface of the brain of a sheep for which we have CT and MIR scan data for an FE model of impact and injury. Thankyou Jeffrey Dutschke

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Problem met on fsfast tutorial data
by lan lin 09 Aug '07

09 Aug '07

I followed the Fsfasttutorial to learn fsfast. But when I run tkregister-sess -s mgh-101.1 -regheader, I always get such error message tkregister-sess logfile is /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/log/tkregister- sess.log -------------------------------------------------------------- Session: /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/mgh-101.1---------------- Thu Aug 9 15:19:10 MST 2007 ERROR: fbph1-101 is not in SUBJECTS_DIR SUBJECTS_DIR is /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study thanks

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RE: [Freesurfer] determining sizes of clusters at given CWP cutoff
by Don Hagler 09 Aug '07

09 Aug '07

There is no reason why you shouldn't be able to get the cut-off size from monte carlo simulations. It just depends on the program you use to do it. For example, AFNI's AlphaSim gives cluster sizes as a function of corrected p-value. By the way, monte carlo simulations are a waste of time. Keith Worsley's "Random Field Theory" method (http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m) can be used to directly (in seconds) estimate the cluster size thresholds given: total surface area number of vertices fwhm smoothness I've found (Hagler et al., Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data, NeuroImage, 2006) that RFT and monte carlo simulations give practically identical results. See the attached matlab script for a wrapper around Worsley's code to calculate the cluster size thresholds using RFT. >From: Robert Levy <levy(a)nmr.mgh.harvard.edu> >To: Freesurfer(a)nmr.mgh.harvard.edu >Subject: [Freesurfer] determining sizes of clusters at given CWP cutoff >Date: Fri, 03 Aug 2007 11:44:33 -0400 > >Hi, > >I was trying to figure out if there is any way to determine the exact size >at which clusters becomes significant given a specified significance, and >it appeared from the mc-corrected overlay that in this overlay the clusters >do not continously change in size but appear discretely at a given >threshold and are the same size at higher thresholds in an all-or-nother >sort of way. I take this to mean that because the monte carlo simulation >was performed at a given threshold, the clusters at that threshold size are >corrected for mutiple comparisons based on the probability distribution of >the chance data (though I don't know the details). Because it is done in >this way, it seems I would either have to run several monte carlo >simulations, at successively higher minimum thresholds, in order to arrive >at the critical cutoff sizes for significance. This is impractical, so I >guess my question is, does the way in which the monte carlo simulations are >done preclude the possibility of getting the cluster sizes at which they >will have a certain CWP value, or is there some way of doing this? > >Thanks, >Rob > >-- > >Robert P. Levy, B.A. >Research Assistant, Manoach Lab >Massachusetts General Hospital >Charlestown Navy Yard >149 13th St., Room 2611 >Charlestown, MA 02129 >email: levy(a)nmr.mgh.harvard.edu >phone: 617-726-1908 >fax: 617-726-4078 > >http://nmr.mgh.harvard.edu/manoachlab > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Messenger Café open for fun 24/7. Hot games, cool activities served daily. Visit now. http://cafemessenger.com?ocid=TXT_TAGHM_AugHMtagline

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mri_watershed
by nima＠nmr.mgh.harvard.edu 08 Aug '07

08 Aug '07

hi, Under freesurfer, how can I force mri_watershed to create 5012 triangles (ico 4) instead of 20480? cheers nima

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Preproc-sess failed for tutorial data
by lan lin 08 Aug '07

08 Aug '07

I followed the Fsfasttutorial to learn fsfast. But when I run preprocessing (preproc-sess -s mgh-101.1 -fwhm 5), I always get following error message /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/mgh-101.1 cat: seq.info: No such file or directory cat: seq.info: No such file or directory cat: seq.info: No such file or directory ERROR: seq.info file does not appear to be formated correctly Try running fixseqinfo-sess. ERROR: mc-sess failed thanks Lan

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Number of voxels that intersect with inflated brain surface
by raij＠nmr.mgh.harvard.edu 08 Aug '07

08 Aug '07

Dear FreeSurfers, Is there a way to estimate the number of fMRI voxels that intersect with the FreeSurfer anatomical inflated surface space? -"- for a given surface label? We need this as N for calculations of statistical significances (to correct for the oversampling of the orginal 3D voxel space by very densely spaced vertex points on the surface). For this purpose, the voxel size was 3.125 x 3.125 x 4.4 mm, the FOV covered the entire brain, and the anatomical brain is "fsaverage". Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Question about aseg.mgz
by jorge luis 08 Aug '07

08 Aug '07

Hello all Are the norm.mgz and aseg.mgz volumes already aligned to talairach standard space ? I have read on the freesurfer tutorial that the transformation is computed and stored in transforms/talairach.ita but it is no applied to the initial volume. I would like to get the segmentation results aligned to talairach space. In advance thank you very much ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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Question about functional analysis on freesurfer
by lan lin 07 Aug '07

07 Aug '07

I know in freesurfer, the functional statistical analysis is performed on fsl. Could I use freesurfer to analysis the functional data instead of fsl?

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(no subject)
by Lisa Ronan 07 Aug '07

07 Aug '07

Hi All, I am interested in creating a surface label for the temporal lobe. I have tried running the mri_annotation2label calling the aparc.a2005s annotations, then merging the appropriate labels. The process sees to work fine except no label is made for S_temporal_superior. I understand from the --help that "if there are no points in the annotation file for a particular index, no label file is created", but I'm not quite sure what this means. There are stats generated for this region so I'm not sure what's going wrong. I would be grateful for any help on this. Kind regards, Lisa Ronan

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