Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

recon-all issue
by Timothy O'Keefe 15 Jul '05

15 Jul '05

First, I am a newcomer to the FreeSurfer community so bear with me. I have installed a snapshot of FreeSurfer for OSX: freesurfer-Darwin- tiger-full.dmg I seem to have everything working fine in terms of environment settings etc. I created a subject directory and populated it with some T1 data using mksubjdirs and mri_convert (from an AFNI BRIK). Now, upon running recon-all -sid <whatever> -stage1 I receive this output: INFO: SUBJECTS_DIR is /blah/blah/blah ######################################## 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/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/ minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ !p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ ####################################### ERROR: cannot determine format of input So, I decided maybe I should just write my own script to run the commands visible through the csurf GUI logfile. I was able to script up everything except when I hit the mri_fill() point, I receive this error: .... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find pons No such file or directory Does anyone have any suggestions? -T

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Skull stripping
by Fornito, Alexander 15 Jul '05

15 Jul '05

Hi, recon-all stage1 overstrips some of my images during the skull-stripping stage. I've played with the different options, but they don't seem to make any difference at all. Any suggestions? I've tried feeding in a pre-stripped brain (stripped using BET), but the intensity normalization doesn't seem to do to well (ie., although it finishes without error, the wm values are not very uniform, and the segmentation misses large portions of wm). Thanks, Alex

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Tksurfer: Unable to view .orig file
by Arvind Gururajan 14 Jul '05

14 Jul '05

Hi, I have trouble viewing .orig files in Tksurfer. I used mris_convert to generate .orig files from .ascii( with number of vertices and triangles for each hemisphere). Any quick thoughts on what could be wrong ? No error messages. Help would be appreciated. Arvind Gururajan

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Center and radius of qsphere surface
by Ngo Trung Thanh 14 Jul '05

14 Jul '05

Hi, How can we know the center and radius of the sphere surface in qsphere files? I guess that the center is (0,0,0) (RAS), what about the radius? Thanks. Best, ntt __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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RE: [Freesurfer] Anatomical stats for labels
by Fornito, Alexander 13 Jul '05

13 Jul '05

Right, so if vertex 'i' is labelled on the white surface, then vertex 'i' will be labelled on the pial surface, and no additional vertices will be labelled on the pial surface (ie., no new ones that are not labelled on the wm surface?). In that case differences is in surface area between the white and pial come about as a result of shearing forces as the wm surface is deformed outward. Is that correct? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 7/14/2005 8:04 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Anatomical stats for labels the label is identified by the vertex indices, which allow it to be projected onto any surface. On Thu, 14 Jul 2005, Fornito, Alexander wrote: > Makes sense. If the lable is only defined along the wm surface, how are the pial surface vertices defined/identified? > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 7/13/2005 9:32 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Anatomical stats for labels > > > > yes, if you specify pial it will be the pial surface area. > > On Wed, 13 Jul > 2005, Fornito, Alexander wrote: > > > Cool, thanks. > > On this issue, I've noticed that lables are defined along the wm surface (eg., when you load them in tkmedit, they do not appear long the pial surface). As such, when I assume that "total surface area" in mris_anatomical_stats corresponds to the area of this specified wm surface when white is specified as the surface in the command line. If pial is specified, does "total surface area" refer to the surface area of the pial surface defined by the vertices linked to those on the wm surface label (ie., those that were deformed out from the wm), or does it refer to a surface selected by some other means? I have some manually delineated labels (obtained from 3D overlays) that cover the wm surface of the area I'm interested in, but am unsure of the extent to which I need to worry about what parts of the pial surface (or intermediate gm) is included. > > Hope this makes sense! > > Thanks, > > Alex > > > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Tue 7/12/2005 1:09 AM > > To: Fornito, Alexander > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Anatomical stats for labels > > Hi Alex, > > > > that's a bug - the volume is the total of the surface area of each > > triangle times the average thickness there, so the pial will be different > > from the white (should just take the average of the two) > > > > Bruce > > > > On Mon, 11 Jul 2005, Fornito, Alexander wrote: > > > >> 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 > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > > > > > > > > > > > > >

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RE: [Freesurfer] Anatomical stats for labels
by Fornito, Alexander 13 Jul '05

13 Jul '05

Makes sense. If the lable is only defined along the wm surface, how are the pial surface vertices defined/identified? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 7/13/2005 9:32 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Anatomical stats for labels yes, if you specify pial it will be the pial surface area. On Wed, 13 Jul 2005, Fornito, Alexander wrote: > Cool, thanks. > On this issue, I've noticed that lables are defined along the wm surface (eg., when you load them in tkmedit, they do not appear long the pial surface). As such, when I assume that "total surface area" in mris_anatomical_stats corresponds to the area of this specified wm surface when white is specified as the surface in the command line. If pial is specified, does "total surface area" refer to the surface area of the pial surface defined by the vertices linked to those on the wm surface label (ie., those that were deformed out from the wm), or does it refer to a surface selected by some other means? I have some manually delineated labels (obtained from 3D overlays) that cover the wm surface of the area I'm interested in, but am unsure of the extent to which I need to worry about what parts of the pial surface (or intermediate gm) is included. > Hope this makes sense! > Thanks, > Alex > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Tue 7/12/2005 1:09 AM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Anatomical stats for labels > Hi Alex, > > that's a bug - the volume is the total of the surface area of each > triangle times the average thickness there, so the pial will be different > from the white (should just take the average of the two) > > Bruce > > On Mon, 11 Jul 2005, Fornito, Alexander wrote: > >> 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 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > > > >

2 1

Overlaying / displaying Gaussian curvature
by Rudolph Pienaar 13 Jul '05

13 Jul '05

Hi all - Apologies if this is a simple question, but how can I display the Gaussian curvature on a surface using 'tksurf'? Cheers --R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

2 1

RE: [Freesurfer] Anatomical stats for labels
by Fornito, Alexander 13 Jul '05

13 Jul '05

Cool, thanks. On this issue, I've noticed that lables are defined along the wm surface (eg., when you load them in tkmedit, they do not appear long the pial surface). As such, when I assume that "total surface area" in mris_anatomical_stats corresponds to the area of this specified wm surface when white is specified as the surface in the command line. If pial is specified, does "total surface area" refer to the surface area of the pial surface defined by the vertices linked to those on the wm surface label (ie., those that were deformed out from the wm), or does it refer to a surface selected by some other means? I have some manually delineated labels (obtained from 3D overlays) that cover the wm surface of the area I'm interested in, but am unsure of the extent to which I need to worry about what parts of the pial surface (or intermediate gm) is included. Hope this makes sense! Thanks, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 7/12/2005 1:09 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Anatomical stats for labels Hi Alex, that's a bug - the volume is the total of the surface area of each triangle times the average thickness there, so the pial will be different from the white (should just take the average of the two) Bruce On Mon, 11 Jul 2005, Fornito, Alexander wrote: > 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

2 1

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

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