Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

equipment
by Feng-Xian Yan 09 Nov '07

09 Nov '07

Hi, I want to use freesurfer to quantity cortical thickness, and I want to use the software under Linux fedora core 4. What equipment for computer do you recommend? Think you.

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optseq2 questions
by Susan Mosher 08 Nov '07

08 Nov '07

Greetings Freesurfers, I am using optseq2 for the first time to generate a stimulus order for my trials and figure out the ideal ITI between trials. I have a few questions about how this works. 1. I tried specifying the PSD max as 18 seconds and minimum of 2 seconds. My ntp is 216 and my TR is set at 2 seconds. I have 9 events specified, each 14 seconds long with two repetitions of each. Here is the command I ran: optseq2 --ntp 216 --tr 2 --psdwin 2 18 --ev ev1 14 2 --ev ev2 14 2 --ev ev3 14 2 --ev ev4 14 2 --ev ev5 14 2 --ev ev6 14 2 --ev ev7 14 2 --ev ev8 14 2 --ev ev9 14 2 --o test --nsearch 1000 --nkeep 100 In the par files that are generated, many of the NULL time durations are much longer than the PSD max I specified (i.e., I specified 18 seconds and some are as long as 58 seconds). Is this simply because the duration of my trials is so long that 18 seconds is not long enough of a max PSD? Does optseq2 just ignore my max PSD request if it is unrealistic? 2. Overall, I will have nine runs. While I realize that the mean ITI will remain the same in each par file, I want to minimize the duration of any single given ITI. As such, if I pseudorandomly select only 9 par files with the lowest maximum ITIs, is this acceptable? Is there some reason I would not want to do this? 3. If I wanted to change my TR from 2 seconds to 1.8 seconds, would it be acceptable to use the same trial order/ITI randomizations as I selected that were generated with a 2 second TR, or would I have to generate new ones? This is more a matter of whether I have to make new stimulus lists than running optseq2 again. Many thanks, ~Sue Mosher * * ** *** ***** ******** ************* Susan M. Mosher Program in Neuroscience Boston University 2 Cummington Street, Room 209F Boston, MA 02215-2425 smosher(a)bu.edu * * ** *** ***** ******** *************

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dicom question
by Earl Zastrow 07 Nov '07

07 Nov '07

Hi, I'm a new user and I'm having problem with some of the dicom data sets I have. Namely, I got the following error message when I try to convert some of the data sets to .mgz: file not found or unknown file type for file /home/uwcem/cpratoom/BrainMRI/PA2/SE1/EXP0001.dcm I looked at the dicom info of EXP0001.dcm and discovered that the Manufacturer field is blank, compare to the one that did convert to .mgz without errors. Does that have anything to do with the error that I got? Thank you for your time. Regards, Earl Zastrow -- Earl Zastrow Graduate Research Assistant University of Wisconsin - Madison Computation Electromagnetics Laboratory (UWCEM) cpratoom(a)cae.wisc.edu (608) 265-0651

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skullstripping woes
by Matt Colvin 07 Nov '07

07 Nov '07

Dear FreeSurfer wizards, I have a brain that keeps ending in error during the skullstripping portion of recon1, in version 4.0.1 of freesurfer for linux CentOS. Usually the error is directly preceded by a message about a "Segmentation fault". I have tried tweaking it manually in a couple different ways, including the -multistrip option but so far to no avail. The original message looked like this: ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=154, z=126, r=12861 iterations Segmentation fault Linux tammi 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Oct 29 21:36:33 CST 2007 I have attached a copy of the log if anyone is interested and wants to take a look. As always I would be very grateful is anybody out there has an idea about what is going wrong. --Matt Colvin

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Manual edits to aseg.mgz/brainmask.mgz
by Chris Watson 07 Nov '07

07 Nov '07

Hello all, I was wondering if there is a quick way to make edits to multiple slices of the aseg.mgz (or the brainmask.mgz) volume. Specifically, I am working on my first subject, and it seems that on almost every slice, pieces of the dura/skull/arachnoid/what-have-you get segmented as cortex (less often, pieces of dura are included within the boundary of the pial surface). I've worked on some slices by manually removing/de-segmenting the pixels that need to go, but this is proving to be extraordinarily time-consuming (some of the slices I've worked on can take 10 minutes easily; perhaps I am obsessing too much, but am trying to get it as close to perfect as it should look). For over 100 slices, even 5 minutes/slice of editing will take several hours. I tried changing the mri_watershed parameter on another subject, but that didn't seem to fix anything. Any tips to save me hours will be greatly appreciated. -Chris

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OT - animating ?h.pial or aparc+aseg
by Martin Kavec 07 Nov '07

07 Nov '07

Hi, sorry to bring an off topic, but I could not find a solution myself. I was asked to prepare a short fly-by animation of a ?h.pial for a TV who interviewed my boss last week. Would you have any recommendation on how to do that? The ?h.pial is a mesh, which is ideal, because the surface of the pial would be nice and smooth. I tried to export aparc+aseg to Analyze and read it into OsiriX, where I can easily produce the animation, but the surface was not smooth, as one would expect. So that is not the solution. Has anyone experience with this kind of task? Thanks, Martin

2 3

OpenGL
by Daniel Wakeman 06 Nov '07

06 Nov '07

Hello, I am configuring a Freesurfer installation for two different types of computers (headless servers and workstations). For both sets of computers we want any non-OpenGL commands that are run to first go through python scripts which load balance (these are working fine); however we have directly included the standard tkmedit* tksurfer* tkregister2* scuba* scuba2* and qdec* in the bin directory of freesurfer for the workstations. We still do not seem able to get these applications to work. Are there some dependencies, which I am missing for each of these besides tkmedit.bin etc.? Thank You, Dan

3 2

spmregister on 64 bit
by Doug Greve 06 Nov '07

06 Nov '07

I have spmregister (and spmregister-sess) working on 64 bit machines. The fix is to set the FS_SPMREG_MATLAB to point to the 7.0.1 version of matlab. In the NMR Center, you can just: setenv FS_SPMREG_MATLAB /usr/pubsw/common/matlab/7.0.1/bin/matlab You can do this without affecting the version of matlab that you normally use. This will also work on 32 bit machines. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Matrix ill-conditioned and "yellow brain"
by Juergen Haenggi 06 Nov '07

06 Nov '07

Dear Freesurfer experts We have two problems with FS statistics. One problem occurred when using mri_glmfit: Matrix condition is 11198.7 ERROR: matrix is ill-conditioned or badly scaled, condno = 11198.7 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I inspected the FSGD file but did not find any error! There was a suggestion in the FS archives to look at the design matrix for significant off-diagonal values but the design matrix (X.mat) was not produced Any idea where the problem is? In another contrast the sig.mgh file produced huge values and the whole brain is colored yellow (see attachment). What happens here? Thanks a lot in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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error during watershed
by Matt Colvin 05 Nov '07

05 Nov '07

Hello freesurfer gurus. Recently I was trying to do a fix on a brain that appeared to have a bad skull strip. The T1 was fine but the brainmask volume came out almost totally black, with the surfaces confined to some fuzziness in the corner (appearing very strange in tkmedit). I attempted to fix the skullstrip by adjusting the watershed, using version 4 to remain consistent with our other subjects for whom we did recon1 with version 4 to get better talairachs. Below is the last part of the log. Any ideas? ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=196 y=119 z=233 r=13 first estimation of the main basin volume: 10195 voxels mean intensity too low ! Modification of the image: intensity*10.67 first estimation of the COG coord: x=196 y=119 z=233 r=13 first estimation of the main basin volume: 10195 voxels mri_watershed Error: Interpolation problem in the white matter curve analysis Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Nov 1 16:25:31 CDT 2007

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