Hi,
I am getting a bus error during a group analysis and I wondered if someone could give me some help.
I am running FreSurfer 3.0.5 on an intel Mac (MacBookPro 2.33Ghz, 3Gb, MacOSX 10.4.8). While going through the steps from the web tutorial (with my own data) I am getting the following message:
After the command: mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat
gdfReadHeader: reading age_fsgd.txt INFO: gd2mtx_method is doss Reading source surface /Applications/freesurfer//sub_aging//average/surf/lh.white reading group avg surface area 782 cm^2 from file Reading in average area /Applications/freesurfer//sub_aging//average/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 67091.234375 AvgVtxArea 0.409487 AvgVtxDist 0.738119 StdVtxDist 0.221868
$Id: mri_glmfit.c,v 1.78.2.7 2007/01/23 21:37:47 greve Exp $ cwd /Applications/freesurfer/sub_aging/stats cmdline mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat sysname Darwin hostname Macintosh.local machine i386 user leonardobonilha FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /Applications/freesurfer/sub_aging/stats/lh.age.thickness.10.mgh FSGD age_fsgd.txt glmdir lh.age.glmdir Creating output directory lh.age.glmdir Bus error
Interestingly, I ran the same analysis (with the same data) on another machine (this time a PC running Ubuntu) and it went fine, without any problems.
Thanks for the support
Leo
Leonardo Bonilha MD PhD Research Assistant Professor Dep of Neuropsychiatry and Communication Sciences and Disorders University of South Carolina
____________________________________________________________________________________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/
Leo,
I'd like you to try a 'dev' build of mri_glmfit, which I believe has fixed some byte-endian issues that might be the source of your problem.
goto this site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and copy mri_glmfit.gz to your $FREESURFER_HOME/bin, then type:
cd $FREESURFER_HOME/bin mv mri_glmfit mri_glmfit.old gunzip mri_glmfit.gz chmod a+x mri_glmfit
then rerun your mri_glmfit command.
Nick
On Tue, 2007-02-27 at 20:32 -0800, Leonardo Bonilha wrote:
Hi,
I am getting a bus error during a group analysis and I wondered if someone could give me some help.
I am running FreSurfer 3.0.5 on an intel Mac (MacBookPro 2.33Ghz, 3Gb, MacOSX 10.4.8). While going through the steps from the web tutorial (with my own data) I am getting the following message:
After the command: mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat
gdfReadHeader: reading age_fsgd.txt INFO: gd2mtx_method is doss Reading source surface /Applications/freesurfer//sub_aging//average/surf/lh.white reading group avg surface area 782 cm^2 from file Reading in average area /Applications/freesurfer//sub_aging//average/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 67091.234375 AvgVtxArea 0.409487 AvgVtxDist 0.738119 StdVtxDist 0.221868
$Id: mri_glmfit.c,v 1.78.2.7 2007/01/23 21:37:47 greve Exp $ cwd /Applications/freesurfer/sub_aging/stats cmdline mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat sysname Darwin hostname Macintosh.local machine i386 user leonardobonilha FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /Applications/freesurfer/sub_aging/stats/lh.age.thickness.10.mgh FSGD age_fsgd.txt glmdir lh.age.glmdir Creating output directory lh.age.glmdir Bus error
Interestingly, I ran the same analysis (with the same data) on another machine (this time a PC running Ubuntu) and it went fine, without any problems.
Thanks for the support
Leo
Leonardo Bonilha MD PhD Research Assistant Professor Dep of Neuropsychiatry and Communication Sciences and Disorders University of South Carolina
TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
Excellent - it worked out fine. Thanks
Leo
--- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Leo,
I'd like you to try a 'dev' build of mri_glmfit, which I believe has fixed some byte-endian issues that might be the source of your problem.
goto this site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and copy mri_glmfit.gz to your $FREESURFER_HOME/bin, then type:
cd $FREESURFER_HOME/bin mv mri_glmfit mri_glmfit.old gunzip mri_glmfit.gz chmod a+x mri_glmfit
then rerun your mri_glmfit command.
Nick
On Tue, 2007-02-27 at 20:32 -0800, Leonardo Bonilha wrote:
Hi,
I am getting a bus error during a group analysis
and I
wondered if someone could give me some help.
I am running FreSurfer 3.0.5 on an intel Mac (MacBookPro 2.33Ghz, 3Gb, MacOSX 10.4.8). While
going
through the steps from the web tutorial (with my
own
data) I am getting the following message:
After the command: mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat
gdfReadHeader: reading age_fsgd.txt INFO: gd2mtx_method is doss Reading source surface
/Applications/freesurfer//sub_aging//average/surf/lh.white
reading group avg surface area 782 cm^2 from file Reading in average area
/Applications/freesurfer//sub_aging//average/surf/lh.white.avg.area.mgh
Number of vertices 163842 Number of faces 327680 Total area 67091.234375 AvgVtxArea 0.409487 AvgVtxDist 0.738119 StdVtxDist 0.221868
$Id: mri_glmfit.c,v 1.78.2.7 2007/01/23 21:37:47
greve
Exp $ cwd /Applications/freesurfer/sub_aging/stats cmdline mri_glmfit --y lh.age.thickness.10.mgh
--fsgd
age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat sysname Darwin hostname Macintosh.local machine i386 user leonardobonilha FixVertexAreaFlag = 1 OneSampleGroupMean 0 y
/Applications/freesurfer/sub_aging/stats/lh.age.thickness.10.mgh
FSGD age_fsgd.txt glmdir lh.age.glmdir Creating output directory lh.age.glmdir Bus error
Interestingly, I ran the same analysis (with the
same
data) on another machine (this time a PC running Ubuntu) and it went fine, without any problems.
Thanks for the support
Leo
Leonardo Bonilha MD PhD Research Assistant Professor Dep of Neuropsychiatry and Communication Sciences
and
Disorders University of South Carolina
____________________________________________________________________________________
TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
____________________________________________________________________________________ Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather
Hi Nick and everyone,
Thanks for the support - I am getting a different bus error now, this time when I try to construct a plot from the same data.
Overlying sig.mgh and opening my fsgd work fine, but when I double click on a point in the overlay I get:
surfer: dmin=0.1186, vno=47164, x=6.9745, y=-38.5756, z=64.6996 % surfer: curv=0.010678, fs=0.000000 % surfer: val=-3.292266, val2=0.000000 % surfer: amp=3.292266, angle=180.000000 deg (0.500000) % Bus error
Any thoughts?
Again, thanks for the great help.
Leo
--- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Leo,
I'd like you to try a 'dev' build of mri_glmfit, which I believe has fixed some byte-endian issues that might be the source of your problem.
goto this site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and copy mri_glmfit.gz to your $FREESURFER_HOME/bin, then type:
cd $FREESURFER_HOME/bin mv mri_glmfit mri_glmfit.old gunzip mri_glmfit.gz chmod a+x mri_glmfit
then rerun your mri_glmfit command.
Nick
On Tue, 2007-02-27 at 20:32 -0800, Leonardo Bonilha wrote:
Hi,
I am getting a bus error during a group analysis
and I
wondered if someone could give me some help.
I am running FreSurfer 3.0.5 on an intel Mac (MacBookPro 2.33Ghz, 3Gb, MacOSX 10.4.8). While
going
through the steps from the web tutorial (with my
own
data) I am getting the following message:
After the command: mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat
gdfReadHeader: reading age_fsgd.txt INFO: gd2mtx_method is doss Reading source surface
/Applications/freesurfer//sub_aging//average/surf/lh.white
reading group avg surface area 782 cm^2 from file Reading in average area
/Applications/freesurfer//sub_aging//average/surf/lh.white.avg.area.mgh
Number of vertices 163842 Number of faces 327680 Total area 67091.234375 AvgVtxArea 0.409487 AvgVtxDist 0.738119 StdVtxDist 0.221868
$Id: mri_glmfit.c,v 1.78.2.7 2007/01/23 21:37:47
greve
Exp $ cwd /Applications/freesurfer/sub_aging/stats cmdline mri_glmfit --y lh.age.thickness.10.mgh
--fsgd
age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat sysname Darwin hostname Macintosh.local machine i386 user leonardobonilha FixVertexAreaFlag = 1 OneSampleGroupMean 0 y
/Applications/freesurfer/sub_aging/stats/lh.age.thickness.10.mgh
FSGD age_fsgd.txt glmdir lh.age.glmdir Creating output directory lh.age.glmdir Bus error
Interestingly, I ran the same analysis (with the
same
data) on another machine (this time a PC running Ubuntu) and it went fine, without any problems.
Thanks for the support
Leo
Leonardo Bonilha MD PhD Research Assistant Professor Dep of Neuropsychiatry and Communication Sciences
and
Disorders University of South Carolina
____________________________________________________________________________________
TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
____________________________________________________________________________________ The fish are biting. Get more visitors on your site using Yahoo! Search Marketing. http://searchmarketing.yahoo.com/arp/sponsoredsearch_v2.php
Leo,
I was unable to replicate this problem, but I have posted a 'dev' build of tksurfer.bin that you can try.
goto this site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and copy tksurfer_macintel.bin.gz to your $FREESURFER_HOME/bin,
then type:
mv tksurfer.bin tksurfer.bin.old gunzip tksurfer_macintel.bin.gz mv tksurfer_macintel.bin tksurfer.bin chmod a+x tksurfer_bin
Nick
On Wed, 2007-02-28 at 11:31 -0800, Leonardo Bonilha wrote:
Hi Nick and everyone,
Thanks for the support - I am getting a different bus error now, this time when I try to construct a plot from the same data.
Overlying sig.mgh and opening my fsgd work fine, but when I double click on a point in the overlay I get:
surfer: dmin=0.1186, vno=47164, x=6.9745, y=-38.5756, z=64.6996 % surfer: curv=0.010678, fs=0.000000 % surfer: val=-3.292266, val2=0.000000 % surfer: amp=3.292266, angle=180.000000 deg (0.500000) % Bus error
Any thoughts?
Again, thanks for the great help.
Leo
--- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Leo,
I'd like you to try a 'dev' build of mri_glmfit, which I believe has fixed some byte-endian issues that might be the source of your problem.
goto this site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and copy mri_glmfit.gz to your $FREESURFER_HOME/bin, then type:
cd $FREESURFER_HOME/bin mv mri_glmfit mri_glmfit.old gunzip mri_glmfit.gz chmod a+x mri_glmfit
then rerun your mri_glmfit command.
Nick
On Tue, 2007-02-27 at 20:32 -0800, Leonardo Bonilha wrote:
Hi,
I am getting a bus error during a group analysis
and I
wondered if someone could give me some help.
I am running FreSurfer 3.0.5 on an intel Mac (MacBookPro 2.33Ghz, 3Gb, MacOSX 10.4.8). While
going
through the steps from the web tutorial (with my
own
data) I am getting the following message:
After the command: mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat
gdfReadHeader: reading age_fsgd.txt INFO: gd2mtx_method is doss Reading source surface
/Applications/freesurfer//sub_aging//average/surf/lh.white
reading group avg surface area 782 cm^2 from file Reading in average area
/Applications/freesurfer//sub_aging//average/surf/lh.white.avg.area.mgh
Number of vertices 163842 Number of faces 327680 Total area 67091.234375 AvgVtxArea 0.409487 AvgVtxDist 0.738119 StdVtxDist 0.221868
$Id: mri_glmfit.c,v 1.78.2.7 2007/01/23 21:37:47
greve
Exp $ cwd /Applications/freesurfer/sub_aging/stats cmdline mri_glmfit --y lh.age.thickness.10.mgh
--fsgd
age_fsgd.txt doss --glmdir lh.age.glmdir --surf average lh --C age.mat sysname Darwin hostname Macintosh.local machine i386 user leonardobonilha FixVertexAreaFlag = 1 OneSampleGroupMean 0 y
/Applications/freesurfer/sub_aging/stats/lh.age.thickness.10.mgh
FSGD age_fsgd.txt glmdir lh.age.glmdir Creating output directory lh.age.glmdir Bus error
Interestingly, I ran the same analysis (with the
same
data) on another machine (this time a PC running Ubuntu) and it went fine, without any problems.
Thanks for the support
Leo
Leonardo Bonilha MD PhD Research Assistant Professor Dep of Neuropsychiatry and Communication Sciences
and
Disorders University of South Carolina
TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Nick,
Thanks for taking the time to help me.
It works - and it was my fault - I was trying to open the original fsgd file, rather than the y.fsgd, located in the glmdir.
Best,
Leo
--- Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Leo,
I was unable to replicate this problem, but I have posted a 'dev' build of tksurfer.bin that you can try.
goto this site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and copy tksurfer_macintel.bin.gz to your $FREESURFER_HOME/bin,
then type:
mv tksurfer.bin tksurfer.bin.old gunzip tksurfer_macintel.bin.gz mv tksurfer_macintel.bin tksurfer.bin chmod a+x tksurfer_bin
Nick
On Wed, 2007-02-28 at 11:31 -0800, Leonardo Bonilha wrote:
Hi Nick and everyone,
Thanks for the support - I am getting a different
bus
error now, this time when I try to construct a
plot
from the same data.
Overlying sig.mgh and opening my fsgd work fine,
but
when I double click on a point in the overlay I
get:
surfer: dmin=0.1186, vno=47164, x=6.9745,
y=-38.5756,
z=64.6996 % surfer: curv=0.010678, fs=0.000000 % surfer: val=-3.292266, val2=0.000000 % surfer: amp=3.292266, angle=180.000000 deg (0.500000) % Bus error
Any thoughts?
Again, thanks for the great help.
Leo
--- Nick Schmansky nicks@nmr.mgh.harvard.edu
wrote:
Leo,
I'd like you to try a 'dev' build of mri_glmfit, which I believe has fixed some byte-endian issues that might be the source of your problem.
goto this site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and copy mri_glmfit.gz to your
$FREESURFER_HOME/bin,
then type:
cd $FREESURFER_HOME/bin mv mri_glmfit mri_glmfit.old gunzip mri_glmfit.gz chmod a+x mri_glmfit
then rerun your mri_glmfit command.
Nick
On Tue, 2007-02-27 at 20:32 -0800, Leonardo
Bonilha
wrote:
Hi,
I am getting a bus error during a group
analysis
and I
wondered if someone could give me some help.
I am running FreSurfer 3.0.5 on an intel Mac (MacBookPro 2.33Ghz, 3Gb, MacOSX 10.4.8).
While
going
through the steps from the web tutorial (with
my
own
data) I am getting the following message:
After the command: mri_glmfit --y lh.age.thickness.10.mgh --fsgd age_fsgd.txt doss --glmdir lh.age.glmdir
--surf
average lh --C age.mat
gdfReadHeader: reading age_fsgd.txt INFO: gd2mtx_method is doss Reading source surface
/Applications/freesurfer//sub_aging//average/surf/lh.white
reading group avg surface area 782 cm^2 from
file
Reading in average area
/Applications/freesurfer//sub_aging//average/surf/lh.white.avg.area.mgh
Number of vertices 163842 Number of faces 327680 Total area 67091.234375 AvgVtxArea 0.409487 AvgVtxDist 0.738119 StdVtxDist 0.221868
$Id: mri_glmfit.c,v 1.78.2.7 2007/01/23
21:37:47
greve
Exp $ cwd /Applications/freesurfer/sub_aging/stats cmdline mri_glmfit --y lh.age.thickness.10.mgh
--fsgd
age_fsgd.txt doss --glmdir lh.age.glmdir
--surf
average lh --C age.mat sysname Darwin hostname Macintosh.local machine i386 user leonardobonilha FixVertexAreaFlag = 1 OneSampleGroupMean 0 y
/Applications/freesurfer/sub_aging/stats/lh.age.thickness.10.mgh
FSGD age_fsgd.txt glmdir lh.age.glmdir Creating output directory lh.age.glmdir Bus error
Interestingly, I ran the same analysis (with
the
same
data) on another machine (this time a PC
running
Ubuntu) and it went fine, without any
problems.
Thanks for the support
Leo
Leonardo Bonilha MD PhD Research Assistant Professor Dep of Neuropsychiatry and Communication
Sciences
and
Disorders University of South Carolina
____________________________________________________________________________________
TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
____________________________________________________________________________________
The fish are biting.
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