Re: [Freesurfer] rh and lh neighbour error
check the aseg and see if it's reasonable. Something is badly wrong if there are no lh and rh white matter points that are nbrs. cheers, Bruce On Fri, 6 Jan 2006, Fornito, Alexander wrote: Hi, I've been getting the following error message when running autorecon2-wm with some of my images.Any idea as to what might be causing this? Thanks, Alex Fill Fri Jan 6 14:15:18 EST 2006 Using transforms/talairach.lta mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz /data/flanders/work/alex/freesurfer/subjects_fe/1000795_fixwm/mri logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; mri_fill: could not find any points where lh and rh wm are nbrs INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst reading segmented volume aseg.mgz... INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux recon-all exited with errors at Fri Jan 6 14:16:07 EST 2006 Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: mk-fieldsign problems
hi again
we've been trying various things to get mk-fieldsign to work: installing the
development version of freesurfer and trying it on a different computer, but we
get the same error message. We thought that perhaps mk-fieldsign doesn't have
the same access permissions as the other tcl scripts or that it's not actually
looking in the same directory as for, e.g. tksurfer.tcl for which it gives the
full path:
surfer: using interface /home/jaspell/freesurfer/lib/tcl/tksurfer.tcl
Read /home/jaspell/freesurfer/surface_labels.txt, found 95 structures
tksurfer: run tcl script: mk-fieldsign.tcl
we are still stuck so would be really grateful for any tips!
thanks very much,
Jane
In message <[EMAIL PROTECTED]> Bruce
Fischl <[EMAIL PROTECTED]> writes:
> hmmm, do you have it? If not, I've attached a copy.
>
> cheers,
> Bruc
> e
> On Tue, 3 Jan 2006, Jane Aspell wrote:
>
> > Hi
> >
> > I would be really grateful if someone could help me with the problems I am
> > having with mk-fieldsign. Even after installing a new version of freesurfer
> > and
> > making various changes to libraries etc. when i run:
> > "paint-sess -sf sessid -a rtopy -hemi rh" i get the error below:
> >
> > tksurfer: run tcl script: mk-fieldsign.tcl
> > couldn't read file "mk-fieldsign.tcl": no such file or directory
> >
> > even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which
> > works fine).
> > i am running Red Hat Linux release 9 (Shrike) and installed from
> > freesurfer-Linux-rh9-v2.2.tar.gz
> >
> > any idea what to do?
> > thanks again for your help!
> >
> > Jane
> >
> >
> > In message <[EMAIL PROTECTED]> Nick
> > Schmansky <[EMAIL PROTECTED]> writes:
> >> Jane,
> >>
> >> Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does
> >> not use these libraries any more (I think the older -20040218 release
> >> did, however).
> >>
> >> Do you have the environment variable ITCL_LIBRARY defined in your
> >> startup .cshrc file? You can test if it is set by typing (in csh or
> >> tcsh):
> >>
> >> env|grep ITCL
> >>
> >> If it is set (which it might be, from your older freesurfer
> >> installation), then it should be deleted or commented-out from
> >> your .cshrc (or possibly it was placed in your
> >> $FREESURFER_HOME/SetUpFreeSurfer.csh file).
> >>
> >> You can also just type this:
> >>
> >> unsetenv ITCL_LIBRARY
> >>
> >> and then try tkmedit.
> >>
> >> If this is not the problem, can you tell me which OS you are running?
> >> Type:
> >>
> >> cat /etc/redhat-release
> >>
> >> and
> >>
> >> uname -a
> >>
> >> A last ditch effort is to install the itcl libs, from this site:
> >>
> >> http://rpmfind.net/linux/rpm2html/search.php?query=itcl
> >>
> >> But this should not be necessary, as tkmedit that you have does not use
> >> this library (I am truly puzzled why 'ldd' shows that it needs these
> >> libs).
> >>
> >> Thanks,
> >>
> >> Nick
> >>
> >>
> >> On Mon, 2005-12-12 at 11:40 +, Jane Aspell wrote:
> >>> hi nick
> >>>
> >>> when i type >ldd `which tkmedit` i get the ouput pasted below this email.
> >>> libitk3.2.so and libitcl3.2.so are not found - could be the problem?
> >>>
> >>> uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh
> >>> (and typing 'unsetenv TCLLIBPATH') had no effect.
> >>>
> >>> an earlier version of freesurfer(freesurfer-20040218) didn't give me any
> >>> of
> >>> these problems and tkmedit etc worked fine.
> >>>
> >>> also, does ANYONE know how to interpret the colour coding (for
> >>> fovea/vertical
> >>> meridian etc) produced by the FsFast retinotopy analysis?!
> >>>
> >>> thanks again!
> >>>
> >>> jane
> >>>
> >>>
> ldd `which tkmedit`
> >>> libtix8.1.8.3.so =>
> >>> /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000)
> >>> libtk8.4.so =>
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
> >>> (0x40051000)
> >>> libtcl8.4.so =>
> >>> /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000)
> >>> libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000)
> >>> libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000)
> >>> libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000)
> >>> libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x4021)
> >>> libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000)
> >>> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
> >>> libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000)
> >>> libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000)
> >>> libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x403ce000)
> >>> libtiff.so.3 => /usr/lib/libtiff.so.3 (0x403ed000)
> >>> libcrypt.so.1 => /lib/libcrypt.so.1 (0x4042e000)
> >>> libz.so.1 => /usr/lib/libz.so.1 (0x4045b000)
> >>> libm.so.6 => /lib/tls/libm.so.6 (0x40469000)
> >>> libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4048b000)
> >>> libc.so.6 => /lib/tls/libc.so.6 (0x4200)
> >>>
RE: [Freesurfer] average thickness
Hi, I downloaded the new version of mris_convert, but I’m having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can’t allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.MGH-NMR Center[EMAIL PROTECTED]Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D.MGH-NMR Center[EMAIL PROTECTED]Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] average thickness
what was your command-line? For mris_glm, specify --beta beta.mgh. btw, the rvar output will be the variance of the thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I’m having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can’t allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: mk-fieldsign problems
Hi Jane,
Can you send all the relevant info? See
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
doug
Jane Aspell wrote:
hi again
we've been trying various things to get mk-fieldsign to work: installing the
development version of freesurfer and trying it on a different computer, but we
get the same error message. We thought that perhaps mk-fieldsign doesn't have
the same access permissions as the other tcl scripts or that it's not actually
looking in the same directory as for, e.g. tksurfer.tcl for which it gives the
full path:
surfer: using interface /home/jaspell/freesurfer/lib/tcl/tksurfer.tcl
Read /home/jaspell/freesurfer/surface_labels.txt, found 95 structures
tksurfer: run tcl script: mk-fieldsign.tcl
we are still stuck so would be really grateful for any tips!
thanks very much,
Jane
In message <[EMAIL PROTECTED]> Bruce
Fischl <[EMAIL PROTECTED]> writes:
hmmm, do you have it? If not, I've attached a copy.
cheers,
Bruc
e
On Tue, 3 Jan 2006, Jane Aspell wrote:
Hi
I would be really grateful if someone could help me with the problems I am
having with mk-fieldsign. Even after installing a new version of freesurfer and
making various changes to libraries etc. when i run:
"paint-sess -sf sessid -a rtopy -hemi rh" i get the error below:
tksurfer: run tcl script: mk-fieldsign.tcl
couldn't read file "mk-fieldsign.tcl": no such file or directory
even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which
works fine).
i am running Red Hat Linux release 9 (Shrike) and installed from
freesurfer-Linux-rh9-v2.2.tar.gz
any idea what to do?
thanks again for your help!
Jane
In message <[EMAIL PROTECTED]> Nick
Schmansky <[EMAIL PROTECTED]> writes:
Jane,
Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does
not use these libraries any more (I think the older -20040218 release
did, however).
Do you have the environment variable ITCL_LIBRARY defined in your
startup .cshrc file? You can test if it is set by typing (in csh or
tcsh):
env|grep ITCL
If it is set (which it might be, from your older freesurfer
installation), then it should be deleted or commented-out from
your .cshrc (or possibly it was placed in your
$FREESURFER_HOME/SetUpFreeSurfer.csh file).
You can also just type this:
unsetenv ITCL_LIBRARY
and then try tkmedit.
If this is not the problem, can you tell me which OS you are running?
Type:
cat /etc/redhat-release
and
uname -a
A last ditch effort is to install the itcl libs, from this site:
http://rpmfind.net/linux/rpm2html/search.php?query=itcl
But this should not be necessary, as tkmedit that you have does not use
this library (I am truly puzzled why 'ldd' shows that it needs these
libs).
Thanks,
Nick
On Mon, 2005-12-12 at 11:40 +, Jane Aspell wrote:
hi nick
when i type >ldd `which tkmedit` i get the ouput pasted below this email.
libitk3.2.so and libitcl3.2.so are not found - could be the problem?
uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh
(and typing 'unsetenv TCLLIBPATH') had no effect.
an earlier version of freesurfer(freesurfer-20040218) didn't give me any of
these problems and tkmedit etc worked fine.
also, does ANYONE know how to interpret the colour coding (for fovea/vertical
meridian etc) produced by the FsFast retinotopy analysis?!
thanks again!
jane
ldd `which tkmedit`
libtix8.1.8.3.so =>
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000)
libtk8.4.so =>
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
(0x40051000)
libtcl8.4.so =>
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000)
libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000)
libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000)
libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000)
libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x4021)
libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000)
libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000)
libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x403ce000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0x403ed000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x4042e000)
libz.so.1 => /usr/lib/libz.so.1 (0x4045b000)
libm.so.6 => /lib/tls/libm.so.6 (0x40469000)
libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4048b000)
libc.so.6 => /lib/tls/libc.so.6 (0x4200)
libitk3.2.so => not found
libitcl3.2.so => not found
libdl.so.2 => /lib/libdl.so.2 (0x4049a000)
libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x4049e000)
libXext.so.6 => /usr/X11R6/lib/l
RE: [Freesurfer] average thickness
use mri_convert, not mris_convert (the version with the "s" is for surfaces, not volumes) Bruce On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I'm having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can't allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] average thickness
He wants to convert to the ascii surface format, so he needs mris_convert (which will read all our "volume" formats). Bruce Fischl wrote: use mri_convert, not mris_convert (the version with the "s" is for surfaces, not volumes) Bruce On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I'm having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can't allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] average thickness
it will? Who knew? If they are just your "volume-encoded surface files", then mri_convert should do the job, no? On Fri, 6 Jan 2006, Doug Greve wrote: He wants to convert to the ascii surface format, so he needs mris_convert (which will read all our "volume" formats). Bruce Fischl wrote: use mri_convert, not mris_convert (the version with the "s" is for surfaces, not volumes) Bruce On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I'm having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can't allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] average thickness
mri_convert won't produce ascii surface format, will it? Bruce Fischl wrote: it will? Who knew? If they are just your "volume-encoded surface files", then mri_convert should do the job, no? On Fri, 6 Jan 2006, Doug Greve wrote: He wants to convert to the ascii surface format, so he needs mris_convert (which will read all our "volume" formats). Bruce Fischl wrote: use mri_convert, not mris_convert (the version with the "s" is for surfaces, not volumes) Bruce On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I'm having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can't allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] average thickness
no. On Fri, 6 Jan 2006, Doug Greve wrote: mri_convert won't produce ascii surface format, will it? Bruce Fischl wrote: it will? Who knew? If they are just your "volume-encoded surface files", then mri_convert should do the job, no? On Fri, 6 Jan 2006, Doug Greve wrote: He wants to convert to the ascii surface format, so he needs mris_convert (which will read all our "volume" formats). Bruce Fischl wrote: use mri_convert, not mris_convert (the version with the "s" is for surfaces, not volumes) Bruce On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I'm having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can't allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] stxgrinder - Error using betainc
I'm not sure how to explain this one, so I'll just include the output: [whatever:mystudy] (nmr-std-env) stxgrinder-sess -analysis color01 -contrast color_bw_01 -sf sessid -df sesspar -- stxgrinder-sess logfile is /autofs/space/ship_006/users/kdevaney/Color_Flail/Color_Flail_1/mystudy/log/stxgrinder-sess.060106032655.log -- Contrast List: color_bw_01 MLF is /tmp/stxgrinder-sess-18701.m - < M A T L A B > Copyright 1984-2003 The MathWorks, Inc. Version 6.5.1.199709 Release 13 (Service Pack 1) Aug 4 2003 Using Toolbox Path Cache. Type "help toolbox_path_cache" for more info. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspblks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmasks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmex. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspdemos. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> nthsess = 1 Color_Flail_1 time=0.037307 /autofs/space/ship_006/users/kdevaney/Color_Flail/Color_Flail_1 contrast color_bw_01 (time=0.160157) slice 0 ??? Error using ==> betainc X must be in the interval [0,1]. Error in ==> /usr/local/freesurfer/beta/fsfast/toolbox/tTest.m On line 37 ==> p = betainc(z,dof/2,0.5); Error in ==> /usr/local/freesurfer/beta/fsfast/toolbox/fast_stxgrinder2_sess.m On line 156 ==> prow = sign(trow).*tTest(DOF,abs(trow),tTestDOFMax); >> >> Started at Fri Jan 6 03:26:57 EST 2006 Ended at Fri Jan 6 03:27:05 EST 2006 stxgrinder-sess completed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: mk-fieldsign problems
Can you run paint-sess with the -debug option and send us the output?
On Fri, Jan 06, 2006 at 03:36:50PM +, Jane Aspell wrote:
> hi again
>
> we've been trying various things to get mk-fieldsign to work: installing the
> development version of freesurfer and trying it on a different computer, but
> we
> get the same error message. We thought that perhaps mk-fieldsign doesn't have
> the same access permissions as the other tcl scripts or that it's not actually
> looking in the same directory as for, e.g. tksurfer.tcl for which it gives the
> full path:
>
> surfer: using interface /home/jaspell/freesurfer/lib/tcl/tksurfer.tcl
> Read /home/jaspell/freesurfer/surface_labels.txt, found 95 structures
> tksurfer: run tcl script: mk-fieldsign.tcl
>
> we are still stuck so would be really grateful for any tips!
> thanks very much,
> Jane
>
>
> In message <[EMAIL PROTECTED]> Bruce
> Fischl <[EMAIL PROTECTED]> writes:
> > hmmm, do you have it? If not, I've attached a copy.
> >
> > cheers,
> > Bruc
> > e
> > On Tue, 3 Jan 2006, Jane Aspell wrote:
> >
> > > Hi
> > >
> > > I would be really grateful if someone could help me with the problems I am
> > > having with mk-fieldsign. Even after installing a new version of
> > > freesurfer and
> > > making various changes to libraries etc. when i run:
> > > "paint-sess -sf sessid -a rtopy -hemi rh" i get the error below:
> > >
> > > tksurfer: run tcl script: mk-fieldsign.tcl
> > > couldn't read file "mk-fieldsign.tcl": no such file or directory
> > >
> > > even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl
> > > (which
> > > works fine).
> > > i am running Red Hat Linux release 9 (Shrike) and installed from
> > > freesurfer-Linux-rh9-v2.2.tar.gz
> > >
> > > any idea what to do?
> > > thanks again for your help!
> > >
> > > Jane
> > >
> > >
> > > In message <[EMAIL PROTECTED]> Nick
> > > Schmansky <[EMAIL PROTECTED]> writes:
> > >> Jane,
> > >>
> > >> Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does
> > >> not use these libraries any more (I think the older -20040218 release
> > >> did, however).
> > >>
> > >> Do you have the environment variable ITCL_LIBRARY defined in your
> > >> startup .cshrc file? You can test if it is set by typing (in csh or
> > >> tcsh):
> > >>
> > >> env|grep ITCL
> > >>
> > >> If it is set (which it might be, from your older freesurfer
> > >> installation), then it should be deleted or commented-out from
> > >> your .cshrc (or possibly it was placed in your
> > >> $FREESURFER_HOME/SetUpFreeSurfer.csh file).
> > >>
> > >> You can also just type this:
> > >>
> > >> unsetenv ITCL_LIBRARY
> > >>
> > >> and then try tkmedit.
> > >>
> > >> If this is not the problem, can you tell me which OS you are running?
> > >> Type:
> > >>
> > >> cat /etc/redhat-release
> > >>
> > >> and
> > >>
> > >> uname -a
> > >>
> > >> A last ditch effort is to install the itcl libs, from this site:
> > >>
> > >> http://rpmfind.net/linux/rpm2html/search.php?query=itcl
> > >>
> > >> But this should not be necessary, as tkmedit that you have does not use
> > >> this library (I am truly puzzled why 'ldd' shows that it needs these
> > >> libs).
> > >>
> > >> Thanks,
> > >>
> > >> Nick
> > >>
> > >>
> > >> On Mon, 2005-12-12 at 11:40 +, Jane Aspell wrote:
> > >>> hi nick
> > >>>
> > >>> when i type >ldd `which tkmedit` i get the ouput pasted below this
> > >>> email.
> > >>> libitk3.2.so and libitcl3.2.so are not found - could be the problem?
> > >>>
> > >>> uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in
> > >>> FreeSurferEnv.csh
> > >>> (and typing 'unsetenv TCLLIBPATH') had no effect.
> > >>>
> > >>> an earlier version of freesurfer(freesurfer-20040218) didn't give me
> > >>> any of
> > >>> these problems and tkmedit etc worked fine.
> > >>>
> > >>> also, does ANYONE know how to interpret the colour coding (for
> > >>> fovea/vertical
> > >>> meridian etc) produced by the FsFast retinotopy analysis?!
> > >>>
> > >>> thanks again!
> > >>>
> > >>> jane
> > >>>
> > >>>
> > ldd `which tkmedit`
> > >>> libtix8.1.8.3.so =>
> > >>> /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so
> > >>> (0x40017000)
> > >>> libtk8.4.so =>
> /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
> > >>> (0x40051000)
> > >>> libtcl8.4.so =>
> > >>> /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000)
> > >>> libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000)
> > >>> libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000)
> > >>> libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000)
> > >>> libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x4021)
> > >>> libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000)
> > >>> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
> > >>> libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000)
> > >>> libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000)
> > >>>
RE: [Freesurfer] average thickness
The command line is: mris_glm --design $df --surfmeas thickness --hemi $h --trgsubj $ts --nsmooth 300 --beta beta.mgh --var var.mgh And each column of the design file is: subject_name 1 And then, when I try to run mris_convert -c beta.mgh beta.asc, it just gives me the usage instruction line. When I take out the -c, it does a segmentation fault. Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Friday, January 06, 2006 12:00 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness what was your command-line? For mris_glm, specify --beta beta.mgh. btw, the rvar output will be the variance of the thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I’m having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can’t allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.MGH-NMR Center[EMAIL PROTECTED]Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D.MGH-NMR Center[EMAIL PROTECTED]Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D.MGH-NMR Center[EMAIL PROTECTED]Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_mask bug
Hi, We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz) on RedHat 9 and encountered a problem with the command mri_mask. It is not at all working. Here is what we entered as input: mri_mask input.mgz mask.mgz output.mgz No matter what we put as the mask, the input.mgz and output.mgz are always identical. Is there a bug with this command? (The command says "writing masked volume to output.mgz..." then about 10 seconds later it's done - although nothing is done). Thanks. --Yuhong = Yuhong Jiang[EMAIL PROTECTED] 617-876-2054http://web.mit.edu/yuhong/www = ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_mask bug
what is in the mask.mgz volume? On Fri, 6 Jan 2006, Yuhong Jiang wrote: Hi, We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz) on RedHat 9 and encountered a problem with the command mri_mask. It is not at all working. Here is what we entered as input: mri_mask input.mgz mask.mgz output.mgz No matter what we put as the mask, the input.mgz and output.mgz are always identical. Is there a bug with this command? (The command says "writing masked volume to output.mgz..." then about 10 seconds later it's done - although nothing is done). Thanks. --Yuhong = Yuhong Jiang[EMAIL PROTECTED] 617-876-2054http://web.mit.edu/yuhong/www = ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Scientific Linux vs. Fedora Core
Hello everybody, Does anybody have any experience with Scientific Linux? How does it compare with Fedora Core in terms of computational performance? Will I still be able to use Red Hat FreeSurfer release on a PC running Scientific Linux? Thank you. Regards, Renat. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Scientific Linux vs. Fedora Core
Renat, We do not use Scientific Linux here at MGH, but we do use Centos4, which is an Enterprise Linux variant. We use release 4.2, for both the 32bit and 64bit platforms, so our Centos4 Freesurfer releases should be compatible with Scientific Linux. (Also, Centos4 is based on kernel-2.6.9, as is Scientific Linux). Nick On Fri, 2006-01-06 at 14:05 -1000, Renat Yakupov wrote: > Hello everybody, > > > > Does anybody have any experience with Scientific Linux? How does it > compare with > > Fedora Core in terms of computational performance? > > Will I still be able to use Red Hat FreeSurfer release on a PC running > Scientific Linux? > > Thank you. > > > > Regards, > > Renat. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: mri_mask bug
Hi Bruce, The exact input is: mri_mask T1.mgz brain.mgz brain.mgz This command was invoked by "recon-all -subjid subject -normalization2", which is part of "recon-all -subjid subject -autorecon2". Because of the bug, after this command, the manual edited brain.mgz went back to pre-manual editing state. It appears that by adding a threshold (mri_mask -T 20 T1.mgz brain.mgz brain.mgz) the mask is properly executed. However, this does mean that one cannot run autorecon2 or normalization2, which calls for mri_mask without specifying a threshold. Perhaps someone should fix this command (as well as autorecon2 and normalization2)?? --Yuhong = Yuhong Jiang[EMAIL PROTECTED] 617-876-2054http://web.mit.edu/yuhong/www = ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] inorm-sess trouble
Hi all, I posted a message earlier today from the end of my rope and I think it was a bit terse. Apologies. I'm hoping that someone might have some insight into a (different) problem that's come up with inorm. I'm analyzing three identical subjects. The first two went through fine, but the third is running into an error when I try to run inorm. I'm not sure what is causing this and I'm hoping someone has seen it before or can understand what is going wrong. Any help would be much appreciated. Thanks, Kathryn [whatever:mystudy] (nmr-std-env) inorm-sess -sf sessid -df sesspar -fsd bold -funcstem fmc -motioncor /autofs/space/annecy_014/users/kdevaney/color_flail/cf3 Fri Jan 6 22:19:26 EST 2006 Filesystem 1K-blocks Used Available Use% Mounted on annecy:/local_mount/space/annecy/14 127983336 3073920 124909416 3% /autofs/space/annecy_014 RunList 007 008 009 010 011 012 013 014 set: No match. [whatever:mystudy] (nmr-std-env) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
