Freesurfer June 2005

freesurfer@nmr.mgh.harvard.edu

35 participants
66 discussions

RE: [Freesurfer] mris_glm
by Fornito, Alexander 28 Jun '05

28 Jun '05

Thanks - that got it working! I tried running it on a small sample of 8 subjects, and got a segmentation fault (below). I've noticed that make_average_surface requires subject names to start with a letter. My subjects were coded as numbers, so I just added an 's' to the beginning to get it going. I'm not sure if this has anything to do with the problem. Any help is appreciated. Alex make_average_surface --subjects s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 ==================== make_average_surface ==================== input subjects: s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 output subject: average mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory mris_make_average_surface... reading vertex positions from orig... processing subject s1000186... The following must be revisited********************************** Segmentation fault -----Original Message----- From: Itamar Kahn [mailto:kahn@MIT.EDU] Sent: Tue 6/28/2005 9:51 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] mris_glm The 'make_average_surface' script is in Dos format. You can use the 'dos2unix' application to remove the offending characters from it (dos2unix comes with all linux dist and you can use fink to download it for mac os x). Cheers, Itamar ------------------------- [kahn@###### kahn]$ dos2unix --help dos2unix Copyright (c) 1994-1995 Benjamin Lin Copyright (c) 1998 Bernd Johannes Wuebben (Version 3.0) Copyright (c) 1998 Christian Wurll (Version 3.1) Usage: dos2unix [-hkqV] [-c convmode] [-o file ...] [-n infile outfile ...] -h --help give this help -k --keepdate keep output file date -q --quiet quiet mode, suppress all warnings always on in stdin->stdout mode -V --version display version number -c --convmode conversion mode convmode ASCII, 7bit, ISO, Mac, default to ASCII -l --newline add additional newline in all but Mac convmode -o --oldfile write to old file file ... files to convert in old file mode -n --newfile write to new file infile original file in new file mode outfile output file in new file mode On Jun 27, 2005, at 4:39 PM, Fornito, Alexander wrote: > Hi Nick, > I copied the script into > the bin dir, but when I type make_average_surface, I get the > following: > > make_average_surface > 'nknown option: `- > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. > > Is this normal? > Thanks, > Alex > > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Tue 6/21/2005 11:00 PM > To: Fornito, Alexander > Cc: Freesurfer Mailing List; Bruce Fischl > Subject: RE: [Freesurfer] mris_glm > Alex, > > Attached is the make_average_surface script. Copy it to the > freesurfer/bin directory, and be sure to make it executable (run > 'chmod > 755 make_average_surface' in the freesurfer/bin directory). > > Type 'make_average_surface' to get help. Basically, just the subject > names are required. By default, a 'subject' named 'average' will be > created from your set of subjects (a name instead of 'average' can be > specified on the command line). > > Nick > > ps. I am working on the mris_surface seg-fault problem using the > rh.orig > file that you sent. > > > On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: > >> Hi Alex, >> >> you're better off using the make_average_surfaces.csh script to >> make an >> average of your subjects. Nick: can you send Alex a copy? >> >> thanks, >> Bruce >> On Tue, 21 Jun >> 2005, Fornito, Alexander wrote: >> >> >>> Def. sounds worth doing then! I'll give it a try. >>> My other question is, where can I get my hands on the average7? It's >>> used as the target in the mris_glm examples, but I haven't been >>> able to >>> find the actual average7 surface in any of the freesurfer >>> directories. >>> Am I missing something? >>> Thanks again, >>> Alex >>> >>> -----Original Message----- >>> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] >>> Sent: Tuesday, June 21, 2005 4:11 PM >>> To: Fornito, Alexander >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] mris_glm >>> >>> >>> You can run with just the design matrix, but you won't be able to >>> use >>> the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a >>> way to >>> specify how to build the des mtx. The fsgdf keeps track of what the >>> regressors mean (eg, Age, Class, IQ, etc). When you save the >>> preprocessed data with --y, you'll see that there will be an fsgdf >>> file saved with it. Load this in tksurfer, click on a point, and you >>> will be able to make a scatter plot of, say, thickness vs age, with >>> each class (eg, Male, Female) having a different color dot in the >>> scatter plot. When you mouse-over the dot, it tells you the subject >>> name. Click on a new point and you'll see the scatter plot for that >>> point. If you use --xmat, you can save the design matrix (in >>> matlab-4 >>> format). >>> >>> doug >>> >>> >>> On Tue, 21 Jun 2005, Fornito, Alexander wrote: >>> >>> >>>> Hi, >>>> >>>> I was seeking some clarification re: the relationship between the >>>> >>> fsgdf >>> >>>> and design matrix file for use with mris_glm. It seems to me >>>> that the >>>> two contain very similar info, the examples in the -help don't >>>> use the >>>> fsdf at all. Is it necessary to create one, or can you just run an >>>> analysis with the desmtx? >>>> >>>> Thanks, >>>> >>>> Alex >>>> >>>> >>>> >>>> Alexander Fornito >>>> >>>> M.psych (Clin. Neuro.)/PhD candidate >>>> >>>> Melbourne Neuropsychiatry Centre and Department of Psychology >>>> >>>> The University of Melbourne >>>> >>>> alexander.fornito(a)wh.org.au >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _________________________________________________ Itamar Kahn Department of Psychology Stanford University Jordan Hall, Bldg 420 Mail Code 2130 Stanford, CA 94305 office: 650-724-9515 fax: 650-725-5699 url: http://web.mit.edu/kahn/www _________________________________________________

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Getting there but still stuck
by David Soscia 28 Jun '05

28 Jun '05

Hey guys, I sent one messge before but it was very vague, but now that I am a little bit more knowledgeable about what I am doing, let me be more specific. I have a bunch of images (individual slices) in .dcm format. What EXACTLY should I type in the command line to convert these to .cor files? I've been fiddling with the mri_convert command, and I thought it worked at first, but the files themselves didn't say .cor after I was finished with the "conversion." Also, should I FIRST move the files into an orig directory that I have created, THEN convert them, visa versa, or does it not matter what order I do that in? When I convert the files, I dont know how to convert ALL of the slices in the folder, but I was rather trying to individually convert the files at first, which would take forever. I have gotten several errors wheile trying to convert, but mostly I get ones having to do with the output I am putting into the command. One more thing. Suppose this converion/moving the files works...I am confused as to why you need to make subdirectories under the orig directory labled 001 002 003. Are there more than just 3 I am supposed to make, and what exactly do I put in these subcategories? Once I get over this road block I should be alright because I was able to do everything properly with the bert file. Thanks. Dave

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RE: [Freesurfer] mris_glm
by Fornito, Alexander 27 Jun '05

27 Jun '05

Hi Nick, I copied the script into the bin dir, but when I type make_average_surface, I get the following: make_average_surface 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. Is this normal? Thanks, Alex -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tue 6/21/2005 11:00 PM To: Fornito, Alexander Cc: Freesurfer Mailing List; Bruce Fischl Subject: RE: [Freesurfer] mris_glm Alex, Attached is the make_average_surface script. Copy it to the freesurfer/bin directory, and be sure to make it executable (run 'chmod 755 make_average_surface' in the freesurfer/bin directory). Type 'make_average_surface' to get help. Basically, just the subject names are required. By default, a 'subject' named 'average' will be created from your set of subjects (a name instead of 'average' can be specified on the command line). Nick ps. I am working on the mris_surface seg-fault problem using the rh.orig file that you sent. On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: > Hi Alex, > > you're better off using the make_average_surfaces.csh script to make an > average of your subjects. Nick: can you send Alex a copy? > > thanks, > Bruce > On Tue, 21 Jun > 2005, Fornito, Alexander wrote: > > > Def. sounds worth doing then! I'll give it a try. > > My other question is, where can I get my hands on the average7? It's > > used as the target in the mris_glm examples, but I haven't been able to > > find the actual average7 surface in any of the freesurfer directories. > > Am I missing something? > > Thanks again, > > Alex > > > > -----Original Message----- > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > Sent: Tuesday, June 21, 2005 4:11 PM > > To: Fornito, Alexander > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] mris_glm > > > > > > You can run with just the design matrix, but you won't be able to use > > the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to > > specify how to build the des mtx. The fsgdf keeps track of what the > > regressors mean (eg, Age, Class, IQ, etc). When you save the > > preprocessed data with --y, you'll see that there will be an fsgdf > > file saved with it. Load this in tksurfer, click on a point, and you > > will be able to make a scatter plot of, say, thickness vs age, with > > each class (eg, Male, Female) having a different color dot in the > > scatter plot. When you mouse-over the dot, it tells you the subject > > name. Click on a new point and you'll see the scatter plot for that > > point. If you use --xmat, you can save the design matrix (in matlab-4 > > format). > > > > doug > > > > > > On Tue, 21 Jun 2005, Fornito, Alexander wrote: > > > >> Hi, > >> > >> I was seeking some clarification re: the relationship between the > > fsgdf > >> and design matrix file for use with mris_glm. It seems to me that the > >> two contain very similar info, the examples in the -help don't use the > >> fsdf at all. Is it necessary to create one, or can you just run an > >> analysis with the desmtx? > >> > >> Thanks, > >> > >> Alex > >> > >> > >> > >> Alexander Fornito > >> > >> M.psych (Clin. Neuro.)/PhD candidate > >> > >> Melbourne Neuropsychiatry Centre and Department of Psychology > >> > >> The University of Melbourne > >> > >> alexander.fornito(a)wh.org.au > >> > >> > >> > >> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freesurfer trouble shooting, anyone help?
by David Soscia 27 Jun '05

27 Jun '05

I am just getting acquianted with the program, and I am running into some difficulties. I have a CD filled with MRI scans in AFNI format (.img, .mat, .BRIK, etc.) and I managed after some time to convert one of my .BRIK files to the .cor extention for Freesurfer. Now I am having trouble opening it. When I go to "open subjects" and try to get to where the file is, is lists a "T1" folder where the folder I have the file in should be, and it will not open. Where can I find this file to open it?...it is still on the CD (that is the location I gave when I converted the file), and also I copied all of the files to another folder on the computer, but when I tried to convert the file from that folder, it did not work. The files that I copied over all now have a pen with a cross through it next to the icon (read only maybe that means?)...I'm not sure because I'm very new with Linux. If anyone can help me, let me know. Thanks, Dave

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re: [Freesurfer] Newbie and some question
by Ngo Trung Thanh 27 Jun '05

27 Jun '05

Thanks a lot. Those really help. However, I don't have the root permission to install those libraries into the required directory. So, I guess that I should use the static version of tkmedit and tksurfer. Could you show me where I can find them? Thanks again. Best, Thanh --- "Bell, Andrew (NIH/NIMH)" <bellah(a)mail.nih.gov> wrote: > Thanh Ngo, > > Welcome to FreeSurfer :) I'm no expert but maybe I > can help. > > I had the same problem (many people have) with the > libtk8.3.so and > libtcl8.3so libraries (I assume you're getting a > "shared library" error). > > Before you try to get the static version to work, > try this: > > Have you searched your computer for these files? > FreeSurfer seems to want > them to be in the /usr/lib directory. If you have > these files but they are > in a different directory, create a symbolic link to > them: > > e.g., if the files are in /opt/tcltk/lib > > cd /usr/lib > ln -s /opt/tcltk/lib/libtk8.3.so libtk8.3.so > ln -s /opt/tcltk/lib/libtcl8.3.so libtcl8.3.so > > > If you don't have these files, you should download > them (make sure you get > version 8.3.x!). If you look on the FreeSurfer > Download page, there is a > link below the table with the main downloads that > takes you to the most > up-to-date binaries. I believe these files are > posted there. > > If you have newer versions of tcl/tk (e.g., 8.4 or > 8.5), you need to install > the older versions as well (make sure to FORCE the > install) -- at least this > was the only way I could get it to work. > > > Hope this helps! > > Andy > > > > Andrew H. Bell, PhD > Laboratory of Brain and Cognition > National Institute of Mental Health > Bethesda, Maryland USA > O: (301) 496-5625 x260 > bellah(a)mail.nih.gov > > > ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com

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mris_make_average_surface
by Fornito, Alexander 26 Jun '05

26 Jun '05

Hi, I'm having a little trouble interpreting the mris_make_average_surface usage and was hpoing for some help: usage: mris_make_average_surface [options] <hemi> <output surf name> <canon surface> <output subject name> <subject> ... <output subject name > this program will generate an average of the orig surfaces of all the subjects specified (unless the -s <surface name> flag is used) the transform defaults to talairach.xfm in the subject's mri/transforms directory, but can be changed using the -x <xform name> switch What does the canon surface refer to? Why is there an ouput subject name for each subject? Why does it avarege the orig, and not final surfaces? Could you please give me an example of a command line? Thanks, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 10:02 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] vertex correspondance they are in correspondence, but there may be shear in the pial deformation, so the link will overestimate the thickness. Easy to compute though, just the distance between the same vertex on the 2 surfaces On Wed, 22 Jun 2005, Fornito, Alexander wrote: > Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch & Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface. > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 6/22/2005 9:20 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] vertex correspondance > > > > Hi Alex, > > yes, all the surfaces of a hemisphere (except qsphere) have the same # of > vertices/edges and faces. I think Doug has something that will sample the > mask. mri_vol2label or something like that? > > Bruce > > > On Wed, 22 Jun 2005, Fornito, Alexander wrote: > > > Hi again, > > > > So many questions!! > > > > Is there some sort of correspondence between vertices on the inner (wm) > > and outer (pial) surfaces? Ie., for every vertex on the inner surface, > > is there a point on the outer surface, and if so, does Freesurfer retain > > this information in any of the files? > > > > > > > > Also, I have some binary masks that I have manually traced using another > > program that I would like to apply to the surfaces to get regional > > measures of thickness. The mask images are in analyze format. Is there > > any way that I can do this? > > > > Thanks as always, > > > > Alex > > > > > > > > > > > > Alexander Fornito > > > > M.psych (Clin. Neuro.)/PhD candidate > > > > Melbourne Neuropsychiatry Centre and Department of Psychology > > > > The University of Melbourne > > > > alexander.fornito(a)wh.org.au > > > > > > > > > > >

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Newbie and some questions
by Ngo Trung Thanh 25 Jun '05

25 Jun '05

Hi, I installed FreeSurfer in Linux and ran some test on my data. The Volume Processing step and Create Surface step ran smoothly. >From the guide, after these steps, I can view the result by clicking on the Volume button and Surface button. But these, two buttons do not work. I tried to run the tkmedit command but it generate an error of loading libtk8.3.so library. I learned that I can use the static version of tkmedit, but it generated the same error. Also, I found that tksurfer.static is missing in the distribution. Could anyone show me how I can fix this problem and where I can find tksurfer.static? Another question is that after the Volume Processing step, there should be some skull stripped data. Is there any ways that I can convert these data into some familiar 3-D image formats, like MINC or Analyze, so that I can view it in another program. Thanks a lot. Best, Thanh Ngo __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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defining labels
by Kirk, Gregory 23 Jun '05

23 Jun '05

Hello, I remember a message from Bruce to use mris_anotomical_stats -l label to generate statistics for a region, but unfortunatly I cannot find how to define a label, docs do not seem to tell, a quick start tip please. G.

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question on documentation
by Glenn Lawyer 22 Jun '05

22 Jun '05

Hi, We just saw a discussion between Alexander, Doug, Bruce, and Nick about mris_glm which mentioned the FSGDF file. I had not heard of using a group descripter file before, as the statistical aspects of Freesurfer are not covered in (my copy of) the manual or tutorial (downloaded from surfer....harvard.edu/docs/ in the last week). I will start using one, as it provides a more elegant approach than a desing matrix. Not knowing how to write a GDF, I did a google search and found this link: http://surfer.nmr.mgh.harvard.edu/docs/fsgdf.txt, which was very informative. This page, however, appears to be an orphan; I could not find a link to it from any page starting from surfer....harvard.edu/. What other documentation is "hidden" in the docs/ section of your web page? I have found all of the freesurfer documentation to be very helpful, but I have not found all of the documentation. +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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Questions regarding monkey reconstructions
by Andrew H Bell 22 Jun '05

22 Jun '05

Fellow FreeSurfers, I have a few (more) questions regarding high-res monkey reconstructions. Forgive my naivete - I'm still quite new to this program: I've managed to strip the skull and surrounding muscle tissue (mri_watershed -r 60 -h 15 -wat <in> <out> did the trick) I am now trying to segment, fill and create surfaces. Questions: 1) What is the relationship between mri_segment and control points? I've added a whole whack of control points but they seem to have no effect on the segmentation. How do I influence the segmentation because I'm missing several areas of white matter. 2) For some reason, when I try to run mri_fill, I get a segmentation fault. I'm using the following command: mri_fill -PV 124 138 116 -CV 124 106 116 wm filled I've also tried to enter the above values for the cutting planes in the EXPERT PREFERENCES (as per the manual) and use the interface to fill the white matter, create surfaces, etc. It runs to completion and splits the two hemispheres ok but lops off the top portion of the left hemisphere. 3) Getting back to control points, I've placed a bunch of control points in white matter that seems to get missed. However, when I look at the result after adding these points, they are hanging in empty space (i.e., they don't seem to have any effect). I'm sure this won't be the last of my questions. I appreciate all the help so far!! Thanks!!!! Andy Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 fax: (301) 402-0921 mobile: (202) 679-1279 bellah(a)mail.nih.gov

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Freesurfer June 2005