Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30051 discussions

tkmedit/tksurfer won't start properly
by N.M. van Strien 18 Jun '04

18 Jun '04

Dear Freesurfer experts, I have installed the snapshot of freesurfer on my computer in order to learn how to create flat maps with functional overlays. The freesurfer interface comes up nicely and data processing seems to work properly. However, until now I have not been able to view the data with tkmedit and tksurfer. I have studied the FAQomatic but have not been able to resolve this problem. In the case of tkmedit it seems as if the program is unable to write to the screen. However no error messages occur, even when run from the command line. It just starts - works for a second or two - and then stops without displaying anything. Tksurfer on the other hand produces to windows on the screen (one with the inflated image), but the window in which the controls should be displayed remains empty and unresponsive. I am running Fedora Core 2 with a kernel that is especially compiled to support the latest nvidia drivers for the geforce 4 graphics board in the system I am working on. I have checked the symlinks to the GL drivers that tkmedit and tksurfer calls and all seems to be properly installed. The static versions of the programs also do not work. Could there be any problem between the GLX drivers from NVIDIA and the freeglut OPENGL utility toolkit (both are the latest version)? Can you give me any suggestion what I could try next in order to get things working? Thank you, drs. Niels M. van Strien Vrije Universiteit Medisch Centrum Department of Anatomy, room MF-G102 b Van der Boechorststraat 7 P.O. Box 7057 1007 MB Amsterdam The Netherlands e-mail: n.vanstrien(a)vumc.nl phone: +31 (20) 4448047

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Percent Signal Change
by Matt Cain 17 Jun '04

17 Jun '04

Greetings, I'm trying to write a script to generate hemodynamic timecourses for particular voxels. I want to imitate the feature in tkmedit where these graphs can be viewed as Percent Signal Change. I know how to generate this for averages across an ROI, but that involves computing the Average Baseline Activity, a quantity which is tied to the size ROI and thus does not make sense to use for a single voxel. Does anyone know what value is used to properly scale the hemodynamic timecourses and how to compute that value? Thanks Matt Cain mcain(a)nmr.mgh.harvard.edu

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(no subject)
by faramir＠brandeis.edu 11 Jun '04

11 Jun '04

I've tried to run "csurf" on both the Ichiban and Bonaire public computers but it will not work, moving the cursor to the next line after I press enter but providing no further response. On the other hand, tkmedit and tksurfer do seem to work. Only recently (two weeks or so) the program had worked using the same path/source which I have in my .cshrc at present. Any help would be appreciated.

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convert label to mask volume
by Josh Snyder 10 Jun '04

10 Jun '04

Does anyone know of a way to convert a label to a mask bvolume consisting of 1s and 0s with same FOV as a target volume?

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FS-FAST license?
by Nick Knouf 09 Jun '04

09 Jun '04

Hi there, What license is FS-FAST available under? There's no mention in the shell scripts or the matlab scripts. In the FS-FAST doc/ directory there's a "license.gnu", but I don't see any reference to this in the rest of the code. If it's available under the Freesurfer license, is there a grant to make derivative works? I don't see any mention of that in the Freesurfer license... Thanks, nick PS The reason I ask is because in developing my own ROI tools, such as froi, I'd like to know whether or not I have to go about things in a "clean-room" fashion; or, if I modify some of the FS-FAST code, I need to know what the license is, e.g., if it's GPL licensed, I have to distribute my code as GPL as well.

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How does mri_synthesize work?
by Nguyen, Thang Q 09 Jun '04

09 Jun '04

Hello all, I was wondering what type of algorithms/process mri_synthesize uses to compute the output. It appears to be a simple addition function because synthesized volumes appear much brighter in intensity than the component volumes. Is this correct? Thanks, Thang ------------------------ Thang Nguyen Psychiatry and Human Behavior - Brain Imaging Center University of California, Irvine This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

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RE: ÄFreesurferÅ Properties needed in registration
by Hämäläinen Janne 08 Jun '04

08 Jun '04

Thanks, this was what we wanted to know. To clarify the whole process, we would still like to briefly confirm something about the second issue (Apologies for our ignorance ;): It seems that mris_make_template could be the method for making the reference surface for the registration, is this right? If so, is there any options that should be known, or does the method produce the needed properties (mean curvature and convexity) automatically from the curvature files of the given subjects? The information printed using '--help' wasn't too extensive :). -Janne -- Janne Hämäläinen Researcher Helsinki University Central Hospital Department of Radiology janne.hamalainen(a)hus.fi -----Original Message----- From: Bruce Fischl To: Hämäläinen Janne Cc: 'freesurferÉnmr.mgh.harvard.edu' Sent: 6/7/2004 8:29 PM Subject: Re: ÄFreesurferÅ Properties needed in registration 1. you'll need the ?h.curv (smoothed mean curvature) and ?h.sulc (convexity, generated by mris_inflate) to morph. 2. The ?h.average.tif are multi-frame tif, with 3 sets of 3 frames. Each set contains mean, variances and dofs for a geometric measure. The 1st set is the curvature of the inflated surface, which is not currently used in the morph. The second set is convexit (sulc) and the third is the smoothed mean curvature. cheers, Bruce On Mon, 7 Jun 2004, Hämäläinen Janne wrote: > Hi, > > We are planning to use some of our own methodology (mainly segmentation > routines) in the Freesurfer pipeline to make cortical thickness analysis > between groups. Related to this, there is two things that would need > clarification. > > 1. In case we would use our own surfaces for analysis, what surface > properties would be needed by the registration software (mris_register) of > Freesurfer, and, more precisely, exactly what curvature files? In the > www-site of Graham Wideman, he presents a data flow chart that tells the > input and output to the number of programs used in the analysis. He has > concluded that the registration would need only the spherical surface file > (rh.sphere or lh.sphere), but that can't be correct, right? Some curvature > information needs to be used, but what? In the article 'High-Resolution > Intersubject Averaging and a Coordinate System for the Cortical Surface' > (HBM 1999) it is said that convexity of the surface can be used. But what is > the property (and curvature file) used in Freesurfer? > > 2. Then we would of course need our own reference surface for registration, > since we are analysing surfaces constructed differently from the default > Freesurfer surfaces. Is there documentation on what data the reference > surface (e.g. the rh.average.tif or lh.average.tif) contains? Our guess is > that there is curvature data included in this surface file. Is that so, and > is there an easy way to create our own reference surface from a set of > subjects? > > Thanks in advance, > > Janne Hämäläinen > > > > -- > Janne Hämäläinen > Researcher > Helsinki University Central Hospital > Department of Radiology > janne.hamalainen(a)hus.fi > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Properties needed in registration
by Hämäläinen Janne 07 Jun '04

07 Jun '04

Hi, We are planning to use some of our own methodology (mainly segmentation routines) in the Freesurfer pipeline to make cortical thickness analysis between groups. Related to this, there is two things that would need clarification. 1. In case we would use our own surfaces for analysis, what surface properties would be needed by the registration software (mris_register) of Freesurfer, and, more precisely, exactly what curvature files? In the www-site of Graham Wideman, he presents a data flow chart that tells the input and output to the number of programs used in the analysis. He has concluded that the registration would need only the spherical surface file (rh.sphere or lh.sphere), but that can't be correct, right? Some curvature information needs to be used, but what? In the article 'High-Resolution Intersubject Averaging and a Coordinate System for the Cortical Surface' (HBM 1999) it is said that convexity of the surface can be used. But what is the property (and curvature file) used in Freesurfer? 2. Then we would of course need our own reference surface for registration, since we are analysing surfaces constructed differently from the default Freesurfer surfaces. Is there documentation on what data the reference surface (e.g. the rh.average.tif or lh.average.tif) contains? Our guess is that there is curvature data included in this surface file. Is that so, and is there an easy way to create our own reference surface from a set of subjects? Thanks in advance, Janne Hämäläinen -- Janne Hämäläinen Researcher Helsinki University Central Hospital Department of Radiology janne.hamalainen(a)hus.fi

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Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 03 Jun '04

03 Jun '04

I am loading the bfloats through tksurfer, not tkmedit, using the File->Load Overlay dialogue window. When I select a bfloat file with the browse button it fills in the full path information. ----- Original Message ----- From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> Date: Thursday, June 3, 2004 3:56 pm Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer > Maybe it's the case that that version of tkmedit can't load > bfloats that > way. Have you tried specifying directory and stem, i.e.: > > /path/to/data/beta_doss-thickness-250-lh > > for beta_doss-thickness-250-lh_000.bfloat? > > > > > I tried a number of other files and got the same error in all cases. > > > > 1) From the same glm analysis, on the same average7 surface: > > beta_doss-thickness-250-lh_000.bfloat > > beta_doss-thickness-250-rh_000.bfloat (in a different session > with the rh surface) > > > > 2) and from a different glm analysis: > > y_doss-thickness-250-lh_000.bfloat (with a different average7 > surface from that study) > > > > > > Are there any others I should try to load? > > > > > > > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > Thanks for your prompt response. > > > > > > > > > Is this the most current version of FreeSurfer? > > > > > > > > We have the 07-24-2003 version, however I am sure that we > saw > > > this working with this version of Freesurfer last summer. If > > > possible we would prefer to stick with our current version and > > > avoid updating and re-installation. > > > > > > > > > > > > > What input are you giving to load the bfloat? > > > > > > > > In tksurfer File->Load Overlay, we specified the file y_doss- > > > thickness-250lh_000.bfloat > > > > > > > > > > > > Robert > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> > > > > Date: Thursday, June 3, 2004 3:10 pm > > > > Subject: Re: [Freesurfer] scatter plot of multiple subjects > > > thickness data in tksurfer > > > > > > > > > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > > > > > Hi Brian, > > > > > > > > > > > > Thanks for the e-mail. Unfortunately we are still > having > > > > > problems getting the graph window to appear. Here is what > we > > > have:> > > > > > > > > 1) > > > > > > > load the y values into tksurfer to see scatter plots. > > > > > > We tried to load the .bfloat file as an overlay, and got > > > this > > > > > message in the log window: > > > > > > > > > > > > sclv_read_bfloat_values: error in FunD_New > > > > > > > > > > > > Not a directory > > > > > > > > > > > > > > > > > > 2) Here are the messages I get in the log window when > > > loading > > > > > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > > > > > > > > > INFO: ignoring tag Creator > > > > > > INFO: ignoring tag SmoothSteps > > > > > > INFO: ignoring tag SUBECTS_DIR > > > > > > INFO: ignoring tag SynthSeed > > > > > > Read one slice only. Did you put all the slices in the > same > > > > > directory?> WARNING: Could not get the graph title. > > > > > > WARNING: Could not get the measurement label. > > > > > > WARNING: Could not get the subject name. > > > > > > WARNING: Could not get the data file name. > > > > > > ERROR: Could not get number of classes. > > > > > > > > > > > > > > > > > > Thanks for your help, > > > > > > > > > > > > Robert > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > -- > > > > > Kevin Teich > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > Kevin Teich > > > > > > > > > > > > > -- > Kevin Teich > > >

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Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 03 Jun '04

03 Jun '04

> Can you load other .bfloat data, or do you get this error whenever > you try to load any .bfloat data? I tried a number of other files and got the same error in all cases. 1) From the same glm analysis, on the same average7 surface: beta_doss-thickness-250-lh_000.bfloat beta_doss-thickness-250-rh_000.bfloat (in a different session with the rh surface) 2) and from a different glm analysis: y_doss-thickness-250-lh_000.bfloat (with a different average7 surface from that study) Are there any others I should try to load? > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > Thanks for your prompt response. > > > > > Is this the most current version of FreeSurfer? > > > > We have the 07-24-2003 version, however I am sure that we saw > this working with this version of Freesurfer last summer. If > possible we would prefer to stick with our current version and > avoid updating and re-installation. > > > > > > > What input are you giving to load the bfloat? > > > > In tksurfer File->Load Overlay, we specified the file y_doss- > thickness-250lh_000.bfloat > > > > > > Robert > > > > > > > > ----- Original Message ----- > > From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> > > Date: Thursday, June 3, 2004 3:10 pm > > Subject: Re: [Freesurfer] scatter plot of multiple subjects > thickness data in tksurfer > > > > > > > > > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > > > > > Hi Brian, > > > > > > > > Thanks for the e-mail. Unfortunately we are still having > > > problems getting the graph window to appear. Here is what we > have:> > > > > > > 1) > > > > > load the y values into tksurfer to see scatter plots. > > > > We tried to load the .bfloat file as an overlay, and got > this > > > message in the log window: > > > > > > > > sclv_read_bfloat_values: error in FunD_New > > > > > > > > Not a directory > > > > > > > > > > > > 2) Here are the messages I get in the log window when > loading > > > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > > > > > INFO: ignoring tag Creator > > > > INFO: ignoring tag SmoothSteps > > > > INFO: ignoring tag SUBECTS_DIR > > > > INFO: ignoring tag SynthSeed > > > > Read one slice only. Did you put all the slices in the same > > > directory?> WARNING: Could not get the graph title. > > > > WARNING: Could not get the measurement label. > > > > WARNING: Could not get the subject name. > > > > WARNING: Could not get the data file name. > > > > ERROR: Could not get number of classes. > > > > > > > > > > > > Thanks for your help, > > > > > > > > Robert > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > > Kevin Teich > > > > > > > > > > > > > > > > -- > Kevin Teich > > >

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Freesurfer