Freesurfer July 2005

freesurfer@nmr.mgh.harvard.edu

39 participants
68 discussions

Failed segmentation
by Bakkour, Akram 12 Jul '05

12 Jul '05

Dear all, I am working on a recent MPRAGE image obtained at MGH. First, we had trouble converting the files, but Dr. Ress converted it to analyze manually, I then used that analyze file in freesurfer. The image has a lot of inhomogeneity and the intensity is variable from the back and front of the brain and also between hemispheres. wmfill includes the cerebellum as RH even if I set the coordinates for the cutting planes in expert preferences. Any suggestions as to what I should try next? Thanks for the help! Regards, Akram.

3 2

MEG data and ASCII format
by Sarah Rugheimer 12 Jul '05

12 Jul '05

Hello, I am trying to display MEG source location data on the surface. Does anybody have detailed information on this? I am looking at page 125 of the FreeSurfer manual and it describes converting from ASCII format to Curvature files, but I have a few questions. Right now, I have the MEG source waveforms and a program to compute the contours of activation through an inverse technique. Is there a specific format of the output for the MEG data? And when I make the ASCII file, what is the starting latency and the vertex index. I have the value and (x,y) coordinates for that value. Is the vertex index related to the coordinates? Thanks, any help is appreciated. Sarah Rugheimer

2 1

problem with recon-all
by Tamara Knutsen 11 Jul '05

11 Jul '05

when i source: Setting up environment for FreeSurfer/FS-FAST FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast SUBJECTS_DIR /space/sake/3/users/inverse/subjects FUNCTIONALS_DIR /usr/local/freesurfer/dev/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib FSL_DIR /usr/pubsw/packages/fsl/current QTDIR /usr/lib/qt3-gcc2.96 setenv SUBJECTS_DIR /space/orsay/2/knutsen and then run: recon-all-nmr -subjid ben -stage4b i get this error: [whatever:knutsen] (nmr-dev-env) recon-all-nmr -subjid jerry -stage4b INFO: SUBJECTS_DIR is /autofs/space/orsay_002/knutsen ######################################## program versions used $Id: recon-all-nmr,v 1.68 2005/07/07 04:59:34 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ERROR: cannot determine format of input When Leeland runs the same thing from his computer, it runs fine. What is wrong with my setup that I cannot run this? Thanks, Tamara

2 1

Anatomical stats for labels
by Fornito, Alexander 11 Jul '05

11 Jul '05

Hi, I've noticed that when I run mris_anatomical stats on a label, I get a different value for "total gray matter volume" if I run it on the pial surface, compared to if I run it on the white surface. Just wondering why this is, how the total gray matter volume is calculated, and which one represents the true gray matter volume? Thanks, Alex

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Re: [Freesurfer] Problem filling labels
by xmeadow＠uchicago.edu 11 Jul '05

11 Jul '05

Hi, I just opened up freesurfer and did some stuff and I got the following in the logs: surfer: using interface /opt/freesurfer_alpha/lib/tcl/tksurfer.new.tcl The /opt/freesurfer_alpha is correct, but I'm not sure what the tksurfer.new.tcl is. Inside freesurfer_alpha/lib I've got a tcl and tcl.new directory. Iniside those folders I've got: tcl.new/tksurfer.new.tcl tcl.new/tksurfer.tcl tcl/tksurfer.new.tcl.020617 tcl/tksurfer.tcl.020318 tcl/tksurfer.tcl tcl/tksurfer.tcl.040219 tcl/tksurfer.new.tcl tcl/tksurfer.tcl.020107 tcl/tksurfer.tcl.120400 But I don't know which of these I should be using. Is there a way I can check which of these is the correct one? Also, in which preference file to I tell Freesurfer to look at the correct tksurfer.tcl file? Thanks very much. >Xander ---- Original message ---- >Date: Fri, 8 Jul 2005 17:35:18 -0400 (EDT) >From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Problem filling labels >To: Xander Meadow <xmeadow(a)uchicago.edu> > > >Actually, I just veried that those are the correct versions to be used >together. > >The only other thing I can think of is that the binary is finding a >different version of the script. When you run tksurfer, look for a line of >output that looks like: > >surfer: using interface .../tksurfer.tcl > >and make sure the .../ part is $FREESURFER_HOME/lib/tcl. Then make sure >that 'which tksurfer' is pointing to the same $FREESURFER_HOME >installation. > > >On Fri, 8 Jul 2005, Xander Meadow wrote: > >> I'm not entirely sure where we got our current version from. If the easiest >> thing to do would be just e-mail me the new script then I am definitely in >> favor of that. I have other machines with freesurfer on them, and it's >> likely they all have this problem, would the easiest thing to do, be to just >> download a new fresh copy of freesurfer from the freesurfer website? But, >> please if it's not too much trouble, send me the new script so I can install >> that and start drawing. Thank you again so much for helping me with this. >> >> >>> Xander >> >> On Jul 8, 2005, at 3:39 PM, Kevin Teich wrote: >> >>> >>> Yes, that version is from 2004, while the script file you're using is from >>> 2003. Did you get a new version from us at some point? If so, you should've >>> gotten a corresponding tksurfer.tcl file. If not, I can give you one. >>> >>> On Fri, 8 Jul 2005, Xander Meadow wrote: >>> >>>>> freesurfer_alpha/bin/tksurfer --all-info >>>> ProgramName: tksurfer ProgramArguments: --all-info ProgramVersion: $Name: >>>> $ TimeStamp: 05/07/08-20:36:58-GMT CVS: $Id: tksurfer.c,v 1.61 2004/01/05 >>>> 20:36:23 fischl Exp $ User: xmeadow Machine: andrew Platform: Linux >>>> PlatformVersion: 2.6.9-11.ELsmp CompilerName: GCC CompilerVersion: 29600 >>>> >>>>> Xander >>>> >>>> On Jul 8, 2005, at 3:26 PM, Kevin Teich wrote: >>>> >>>>> Ah, I think the version of tksurfer you are using is much newer than the >>>>> one that should be associated with the script. What do you get if you >>>>> try: >>>>> tksurfer --all-info >>>>> On Sat, 9 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>> Hi, >>>>>> It used to work in the past, but I don't know what might have >>>>>> changed. The machines run uptodate each night to stay current >>>>>> with Redhat patches, but I'm not sure what might have been >>>>>> updated right before this stopped working. As for tksurfer >>>>>> --version >>>>>> freesurfer_alpha/bin/Linux/tksurfer --version >>>>>> $ >>>>>> I'm not sure what the means though, as it's not a number, just >>>>>> the dollar sign. Does this give you any clues? Thanks so >>>>>> much for helping me out with this. >>>>>>> Xander >>>>>> ---- Original message ---- >>>>>>> Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) >>>>>>> From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >>>>>>> Subject: Re: [Freesurfer] Problem filling labels >>>>>>> To: xmeadow(a)uchicago.edu >>>>>>> I can't duplicate this at all. Has this ever worked for you, >>>>>> or did it >>>>>>> stop working? >>>>>>> Can you give me the output of >>>>>>> tksurfer --version >>>>>>> On Fri, 8 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>>>> In the Fill box the one I am trying to use is "Up to and >>>>>>>> including boundaries" by itself, but I've also tried the other >>>>>>>> possible combinations in a hope that it would work. Also, >>>>>>>> this error always happens regardless of whatever else I've >>>>>> done. >>>>>>>>> Xander >>>>>>>> ---- Original message ---- >>>>>>>>> Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >>>>>>>>> From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >>>>>>>>> Subject: Re: [Freesurfer] Problem filling labels >>>>>>>>> To: Xander Meadow <xmeadow(a)uchicago.edu> >>>>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> What were your settings in the Fill dialog box? Does this >>>>>>>> always happen, >>>>>>>>> or only with a specific combination of options? >>>>>>>>> On Thu, 7 Jul 2005, Xander Meadow wrote: >>>>>>>>>> Hi, >>>>>>>>>> I was trying to make an ROI on an inflated surface. >>>>>>>> Specifically I can >>>>>>>>>> recreate the error if I: >>>>>>>>>> Mark a bunch of vertices >>>>>>>>>> Create fill boundary >>>>>>>>>> clear all marked vertices >>>>>>>>>> mark a vertex within the filled boundary >>>>>>>>>> then try to fill it. >>>>>>>>>> I did all this via the GUI. >>>>>>>>>> Does this help? Is there anything else I can tell you that >>>>>>>> might help? >>>>>>>>>>> Xander >>>>>>>>>> On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >>>>>>>>>>>> Here is the file you requested: >>>>>>>>>>> Hm, that appears to be OK. What action were you performing >>>>>>>> when you got the >>>>>>>>>>> error? >>>>>>>>>>>> Can you send me the file: >>>>>>>>>>>> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >>>>>>>>>>>> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> I'm having trouble filling labels using Freesurfer version >>>>>>>>>>>>> 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked >>>>>>>>>>>>> through the mail archives and found that this problem has >>>>>>>>>>>>> happened in the past, the post is here: >>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html >>>>>>>>>>>>> I get the same error: >>>>>>>>>>>>> Error: Wrong # args: fill_flood_from_cursor >>>>>>>>>>>>> dont_cross_boundary dont_cross_label dont_cross_cmid >>>>>>>>>>>>> dont_cross_fthresh use_multiple_seeds action argument >>>>>>>>>>>>> I have a .xdebug_tkmedit if it would help debug this >>>>>> issue. >>>>>>>>>>>>> Does anyone know what I can do to fix this? Thank you >>>>>>>> very much. >>>>>>>>>>> -- >>>>>>>>>>> Kevin Teich >>>>>>>>> -- >>>>>>>>> Kevin Teich >>>>>>> -- >>>>>>> Kevin Teich >>>>> -- >>>>> Kevin Teich >>>> >>>> >>>> >>> >>> -- >>> Kevin Teich >>> >> >> >> > >-- >Kevin Teich >

3 2

Original surface and sphere correspondence
by Ngo Trung Thanh 10 Jul '05

10 Jul '05

Hi, After mapping the brain surface onto a sphere, we have the surface files. Is there anyway that we can know the correspondence (or the transformation) between the points on the original surface and those on the sphere? Thanks a lot. Best, ntt __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Web tool for visualizing Talairach and MNI locations in 3D volume and on the cortical surface
by David L. Woods 08 Jul '05

08 Jul '05

Freesurfer users who are interested in viewing the location of MNI and Talairach coordinates on the cortical surface or in 3D may be interested in visiting the "Martinez Flat-Mapper" site at http://www.ebire.org/hcnlab/cortical-mapping. Entering MNI or Talairach coordinates will display them on the cortical surface in relation to average gyral anatomy and in a representative 3D brain (Colin). The cortical surface maps are averages of the left and right hemispheres of 40 subjects as viewed with equal area projections that can be centered on temporal, occipital, or frontal lobes. Three different map types are available: cortical curvature, thickness, and fiber directionality (derived from the anisotropic water diffusion). There is also a high-resolution map of average auditory cortex curvature extracted using local landmark techniques. Clicking on a location on any map will display the MNI and Talairach coordinates of the point and show its location in 3D space in the Colin brain. Conversely, clicking on any location in the Colin brain will display that point on the cortical surface maps and provide an estimate of its distance to the gray/white boundary. David L. Woods, Professor of Neurology, Dept. of Neurology,UC Davis, Chief, Clinical Neurophysiology and Chief, Research fMRI imaging, Neurology Service (127E), Building R4, VANCHCS, 150 Muir Rd., Martinez, CA 94553 Tel (925) 372-2571, Fax (925) 229-2315 Email:dlwoods@ucdavis.edu Website: http://marva4.ebire.org/hcnlab

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Re: [Freesurfer] Problem filling labels
by xmeadow＠uchicago.edu 08 Jul '05

08 Jul '05

Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. >Xander ---- Original message ---- >Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) >From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Problem filling labels >To: xmeadow(a)uchicago.edu > > >I can't duplicate this at all. Has this ever worked for you, or did it >stop working? > >Can you give me the output of > >tksurfer --version > >On Fri, 8 Jul 2005 xmeadow(a)uchicago.edu wrote: > >> In the Fill box the one I am trying to use is "Up to and >> including boundaries" by itself, but I've also tried the other >> possible combinations in a hope that it would work. Also, >> this error always happens regardless of whatever else I've done. >> >>> Xander >> >> ---- Original message ---- >>> Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >>> From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Problem filling labels >>> To: Xander Meadow <xmeadow(a)uchicago.edu> >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> >>> What were your settings in the Fill dialog box? Does this >> always happen, >>> or only with a specific combination of options? >>> >>> >>> On Thu, 7 Jul 2005, Xander Meadow wrote: >>> >>>> Hi, >>>> >>>> I was trying to make an ROI on an inflated surface. >> Specifically I can >>>> recreate the error if I: >>>> >>>> Mark a bunch of vertices >>>> Create fill boundary >>>> clear all marked vertices >>>> mark a vertex within the filled boundary >>>> then try to fill it. >>>> >>>> I did all this via the GUI. >>>> >>>> Does this help? Is there anything else I can tell you that >> might help? >>>> >>>>> Xander >>>> >>>> On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >>>> >>>>>> Here is the file you requested: >>>>> >>>>> Hm, that appears to be OK. What action were you performing >> when you got the >>>>> error? >>>>> >>>>> >>>>> >>>>>> Can you send me the file: >>>>>> >>>>>> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >>>>>> >>>>>> >>>>>> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I'm having trouble filling labels using Freesurfer version >>>>>>> 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked >>>>>>> through the mail archives and found that this problem has >>>>>>> happened in the past, the post is here: >>>>>>> >>>>>>> >>>>> >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html >>>>>>> >>>>>>> I get the same error: >>>>>>> >>>>>>> Error: Wrong # args: fill_flood_from_cursor >>>>>>> dont_cross_boundary dont_cross_label dont_cross_cmid >>>>>>> dont_cross_fthresh use_multiple_seeds action argument >>>>>>> >>>>>>> I have a .xdebug_tkmedit if it would help debug this issue. >>>>>>> Does anyone know what I can do to fix this? Thank you >> very much. >>>>>> >>>>> -- >>>>> Kevin Teich >>>>> >>>> >>>> >>>> >>> >>> -- >>> Kevin Teich >>> >> >> >> > >-- >Kevin Teich >

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Re: [Freesurfer] Problem filling labels
by xmeadow＠uchicago.edu 08 Jul '05

08 Jul '05

In the Fill box the one I am trying to use is "Up to and including boundaries" by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. >Xander ---- Original message ---- >Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) >From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Problem filling labels >To: Xander Meadow <xmeadow(a)uchicago.edu> >Cc: freesurfer(a)nmr.mgh.harvard.edu > >What were your settings in the Fill dialog box? Does this always happen, >or only with a specific combination of options? > > >On Thu, 7 Jul 2005, Xander Meadow wrote: > >> Hi, >> >> I was trying to make an ROI on an inflated surface. Specifically I can >> recreate the error if I: >> >> Mark a bunch of vertices >> Create fill boundary >> clear all marked vertices >> mark a vertex within the filled boundary >> then try to fill it. >> >> I did all this via the GUI. >> >> Does this help? Is there anything else I can tell you that might help? >> >>> Xander >> >> On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >> >>>> Here is the file you requested: >>> >>> Hm, that appears to be OK. What action were you performing when you got the >>> error? >>> >>> >>> >>>> Can you send me the file: >>>> >>>> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >>>> >>>> >>>> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >>>> >>>> > Hi, >>>> > >>>> > I'm having trouble filling labels using Freesurfer version >>>> > 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked >>>> > through the mail archives and found that this problem has >>>> > happened in the past, the post is here: >>>> > >>>> > >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html >>>> > >>>> > I get the same error: >>>> > >>>> > Error: Wrong # args: fill_flood_from_cursor >>>> > dont_cross_boundary dont_cross_label dont_cross_cmid >>>> > dont_cross_fthresh use_multiple_seeds action argument >>>> > >>>> > I have a .xdebug_tkmedit if it would help debug this issue. >>>> > Does anyone know what I can do to fix this? Thank you very much. >>>> >>> -- >>> Kevin Teich >>> >> >> >> > >-- >Kevin Teich >

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Re: [Freesurfer] Problem filling labels
by Xander Meadow 07 Jul '05

07 Jul '05

Hi, I was trying to make an ROI on an inflated surface. Specifically I can recreate the error if I: Mark a bunch of vertices Create fill boundary clear all marked vertices mark a vertex within the filled boundary then try to fill it. I did all this via the GUI. Does this help? Is there anything else I can tell you that might help? >Xander On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: >> Here is the file you requested: > > Hm, that appears to be OK. What action were you performing when you > got the error? > > > >> Can you send me the file: >> >> $FREESURFER_HOME/lib/tcl/tksurfer.tcl >> >> >> On Thu, 7 Jul 2005 xmeadow(a)uchicago.edu wrote: >> >> > Hi, >> > >> > I'm having trouble filling labels using Freesurfer version >> > 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked >> > through the mail archives and found that this problem has >> > happened in the past, the post is here: >> > >> > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ > msg00042.html >> > >> > I get the same error: >> > >> > Error: Wrong # args: fill_flood_from_cursor >> > dont_cross_boundary dont_cross_label dont_cross_cmid >> > dont_cross_fthresh use_multiple_seeds action argument >> > >> > I have a .xdebug_tkmedit if it would help debug this issue. >> > Does anyone know what I can do to fix this? Thank you very much. >> > -- > Kevin Teich >

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Freesurfer July 2005