Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

Command for making a picture
by roberto toro 24 Jun '10

24 Jun '10

hello, Is there a command line tool for making a picture of a surface with labels superimposed? thanks in advance! roberto

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RAS to talairach transform
by Corey Keller 23 Jun '10

23 Jun '10

Hi freesurfers, I am trying to convert electrode coordinates from RAS to talairach space. I have 128 electrodes sitting directly on the pial surface which was created from recon-all. I see that the output of each reconstruction has two transforms, talairach.xfm and talairach.auto.xfm. There seems to be a difference between the two - could you explain the difference and which one I should be using? I cannot seem to find this online. Thanks. Best, Corey

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Grey Matter Density?
by Matthew Ku 23 Jun '10

23 Jun '10

Hi Freesurfer Experts, I have been running Freesurfer to calculate the grey matter volume of pediatric brains but I was wondering if there was a method to determine grey matter density using Freesurfer? I have read a question previously posted asking a similar question, but there had been no replies or answers. If there is no command to calculate the density of grey matter, is there any alternate method to determine the density from the volume data? Thanks, Matt _________________________________________ Matthew Ku University of Pennsylvania School of Engineering Class of 2013 (845) 596-3840 mattku(a)seas.upenn.edu

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how to svae FreeSurfer space?
by Guang Zeng 23 Jun '10

23 Jun '10

Hi, there, I have used FreeSurfer cross-sectional and longitudinal stream to process more than 1000 subjects, and the output file occupied almost all my storage space. Currently, I am thinking about delete some FreeSurfer output files to save some storage space, What I am think now is: 1. Delete some mgz files such as rawavg.mgz or orig.mgz which can be regenerate in a short time 2. Keep some files which need lots of time to regenerate such as talairach.m3z. But I am confused by the relationship and dependency of different output file at different stage, does anyone have suggestions? Thanks a lot! Guang _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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Re: [Freesurfer] question about clustering simulation
by Michael Waskom 23 Jun '10

23 Jun '10

Hi Doug, This looks very helpful! Should we use the fwhm size corresponding to the argument of the --fwhm flag when recon-all runs mri_surf2surf (for anatomical stats), or round the measure found in the fwhm.dat of the glmfit dir? Thanks, Mike ---------- Forwarded message ---------- From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: porterj(a)umn.edu Date: Tue, 27 Apr 2010 11:17:24 -0400 Subject: Re: [Freesurfer] question about clustering simulation Yea, that was a bug in the simulation program I used. I did confirm that the simulations were done on the correct hemisphere. Feel free to edit the files. I'll fix the master when I get a chance. doug James Porter wrote: > Doug- > > Let me be the first to say thank you for saving me massive amounts of > simulation time. One bug though: the right hemisphere files say they were > created using the left hemisphere, and mri_surfcluster rejects them. Would > it be verboten to just alter the csd files, or do you have versions that > were created off of fsaverage's right hemisphere? > > matacao:mult-comp-cor porterj$ head > fsaverage/rh/cortex/fwhm19/abs/th33/mc-z.csd > # simtype null-z > # anattype surface fsaverage lh > # FixGroupSubjectArea 1 > # merged 0 > # contrast NA > # seed 1271355821 > # thresh 3.300000 > # threshsign 0.000000 > # searchspace 74490.928733 > # nullfwhm 19.000000 > > Jim Porter, M.A. > Graduate Student > Clinical Science& Psychopathology Research > University of Minnesota > > > On 7/22/64 1:59 PM, Douglas N Greve wrote: > >> 1. Correct on both counts. When I wrote the simulation, I was only trying >> to replicate the random fields analysis. But with a simulation, you have >> more freedom that I am not yet exploiting. >> 2. This is what we are already doing with mc-z >> 3. I'm working on this as well. It turns out that the random fields >> approximation works a lot better when using the number of vertices. >> >> Also, I've run mc-z simulations under a bunch of thresholding and FWHM >> conditions for whole-hemisphere cortex labels. These will be integrated in >> new version of FS, but I've put them here >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor… well. There's a README file in there. This will make running your own >> time-consuming simulations unnecessary (when using the cortex mask at >> least). >> >> doug >> >> Anthony Dick wrote: >> >>> Hello all, >>> >>> I am interested in using the mri_glmfit simulation to control for >>> multiple comparisons in data I have run on the surface in AFNI. Before doing >>> this, I have a few questions: >>> >>> 1. What does the simulation with the mc-z flag do, exactly? It claims to >>> be comparable to AFNI's AlphaSim, but it takes a maximum cluster area for >>> each iteration, which is not exactly what AlphaSim does. Here is my guess: >>> >>> Given a surface, a given smoothness of the data, and a given per-vertex >>> threshold, for each iteration the simulation populates that surface with >>> random data taken from a normal distribution, thresholds the data, and >>> applies the smoothness of the actual data (supplied as an input parameter). >>> It then computes the maximum cluster size in area for that "image". Doing >>> this n iterations gives a distribution of maximum cluster sizes that occur >>> for random data of a given smoothness, and taking cluster sizes above a >>> certain percentile rank controls for the FWE at a level equal to that >>> percentile rank (e.g., 95th% controls for FWE = .05). AlphaSim does >>> something similar, although instead of taking maximum cluster sizes at each >>> iteration it computes all given cluster sizes. AlphaSim also allows for >>> different cluster connectivity radius, but it seems Freesurfer computes only >>> for neighboring vertices. All in all, if this is correct, it seems like a >>> good implementation. >>> >>> 2. It is my understanding that one could bypass running the glm in >>> Freesurfer and only compute the simulation, as the simulation only needs >>> information about the surface, and the smoothness of the data (which are >>> supplied by the user). To do so, you have to "fake out" Freesurfer to bypass >>> glm, but that turns out to be pretty painless. >>> >>> 3. In a future distribution, is it possible to modify this procedure to >>> also output maximum cluster sizes in terms of number of nodes, rather than >>> area? >>> >>> Can you please let me know if I am mistaken in any of these assumptions? >>> Thanks in advance. >>> >>> Anthony >>> >>> >> > > -- 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

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Error while loading shared libraries: libtiff.so.3
by Cindy Eckart 23 Jun '10

23 Jun '10

Dear FreeSurfers, I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a Linux Debian machine (for details see below). After running stable till the -autorecon3 step, the process was killed because the shared library libtiff.so.3 was not found in this distribution. We currently try to fix this problem with a soft link from libtiff.so.4 (and hope that this will suffice to fix the problem) but notwithstanding wanted to ask if there are plans to adapt the FreeSurfer packages to the current libraries to circumvent that problem? Thank you very much for your help! Cindy My machine details: Linux membrane 2.6.26-2-amd64 #1 SMP Tue Mar 9 22:29:32 UTC 2010 x86_64 GNU/Linux Debian version 5.0.4 Shared library: GNU C Library stable release version 2.7, by Roland McGrath et al. Copyright (C) 2007 Free Software Foundation, Inc. Compiled by GNU CC version 4.3.2. Compiled on a Linux >>2.6.26-2-amd64<< system on 2010-01-14. Available extensions: crypt add-on version 2.1 by Michael Glad and others GNU Libidn by Simon Josefsson Native POSIX Threads Library by Ulrich Drepper et al BIND-8.2.3-T5B ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de

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Hemisphere matching problem during MC simulation
by Nick Schmansky 22 Jun '10

22 Jun '10

Dear Freesurfer experts, I have problems concerning the results of a MC simulation. When I checked the results with Qdec I discovered a matching problem for the right hemisphere. It seems like the used command runs the correct analyses for the right hemisphere, but fails projecting it properly to that one. It looks like freesurfer uses atlas and coordinates of the left hemisphere for the right hemisphere. I think the problem starts during MC simulation. Here's a "copy paste" entry of the *.log file, where I think freesurfer clearly mixes up hemisphere information: version $Id: mri_surfcluster.c,v 1.39.2.3 2009/01/15 01:06:01 greve Exp $ hemi = lh srcid = /home/hiwibp14/smb4k/CORTICAL/fmrt/Studie43/freesurfer/qdec/Untitled/rh-Avg-Intercept-thickness/sig.mgh For me obviously in the simulation process the programm mixes up information for right and left hemisphere during the analyses. This happens several times during analyses but only for analyses concerning the right hemisphere (see the complete attached log file). Is there any possibility to specify the command, adressing this problem like a special flag or something? Or is it possible to run the right hemisphere again separately? To run the simulation I used the following command line: mri_glmfit-sim \ --glmdir /home/hiwibp14/smb4k/CORTICAL/fmrt/Studie43/freesurfer/qdec/Untitled \ --sim mc-z 5000 1.3 mc-z.abs.1.3 \ --sim-sign abs \ --overwrite Thanks for your help and best regards, Johanna Feiler ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de

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bbregister with 4.5.0 fsfast
by ythomas 22 Jun '10

22 Jun '10

Hi, I have finished the 4.5.0 fsfast tutorial, and am wondering about the structure-function registration part. Currently, the tutorial recommends: fslregister-sess -s mgh-101.1. I notice that a single register.dat is produced. How are the multiple runs being handled now? Is only the first run used or all the runs are automatically used? I am asking because I would prefer to use bbregister. In bbregister, one passes to bbregister an anatomical subject id and a functional volume. So, (1) Which functional volume should I give to bbregister? (2) Are the functional volumes of the different runs co-registered after I run "preproc-sess"? (3) Presumably, I should also give bbregister the pre-smoothed, but motion corrected functional volume since smoothing would remove the gray-white boundary distinction that bbregister uses? Thanks, Thomas

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ASCII to MGH
by James Porter 21 Jun '10

21 Jun '10

Hello- I know how to use mri_convert and mris_convert to obtain ascii files of thickness values that I can read into stats software, but I'm having trouble going the other direction. Is there a good way to convert ascii lists of vertex values into mgh files so I can view them as overlays or utilize commands like mri_surfcluster? Thanks, Jim -- Jim Porter, M.A. Graduate Student Clinical Science& Psychopathology Research University of Minnesota

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error in running fsfast tutorial
by ythomas 21 Jun '10

21 Jun '10

Hi, I am trying to run the fsfast tutorial, and I am getting the following matlab error: Undefined function or method 'MRIwrite' for input arguments of type 'struct'. I ran the following commands: nexlin7:ythomas[test_fsfast/fsfast-tutorial/my-study] pwd /autofs/cluster/nexus/12/users/ythomas/data/test_fsfast/fsfast- tutorial/my-study nexlin7:ythomas[test_fsfast/fsfast-tutorial/my-study] preproc-sess -s mgh-101.1 -fwhm 6 I tried adding a startup.m file in /autofs/cluster/nexus/12/users/ ythomas/data/test_fsfast/fsfast-tutorial/my-study/startup.m before calling preproc-sess to tell matlab where to find MRIwrite, but that doesn't seem to help. Thanks, Thomas

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Freesurfer June 2010