Hi Bruce,
I've been trying to improve the talairach xfm and try different things with afni, but so far nothing has worked out. The brain still crashes at the skull strip. I fed in the afni skull strip to resume the pipeline from autorecon2 but the segmentation was really bad, with the white matter surface not accurate.
Did you have any suggestions for the background values.
Any ideas.
Thanks,
Anil.
On 2/21/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Anil,
I got the email, but I'm out of town and won't get to it until next week Bruce On Wed, 21 Feb 2007, Anil Roy wrote:
I think my last email didn't get through. Bruce, I've uploaded the
001.mgz.
It should arrive in your mailbox. I can upload it again if there was any problem.
Thanks,
Anil.
On 2/20/07, Anil Roy aroy85@gmail.com wrote:
Its uploaded
On 2/20/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I need the 001.mgz On Tue, 20 Feb 2007, Anil Roy wrote:
Bruce, I had uploaded the orig.mgz for Nick. I think you should
find
the
link below. I can also upload the 001.mgz for you. There are no dicoms because the scan is from a GE scanner (120
slices,
details are below)and all the files are named as I.??? I could also upload these files for you.
Anil.
On 2/20/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu > wrote:
I think it's something afni is doing, but I'm not sure. Did you
give
us
the data before conversion (either the dicoms or the 001.mgz)
On Tue, 20 Feb 2007, Anil Roy wrote:
> Hey Freesurfers, > > I fed freesurfer the brainmask.mgz generated by AFNI. autorecon2
and
> autorecon3 ran fine with no errors but the resulting surfaces
are
not
very > accurate. > > Bruce, you mentioned that my background values were too high. Is
there a
way > to reduce them so that freesurfer can do the watershed without
any
glitches. > > Thanks, > > Anil. > > On 2/15/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: >> >> I think it's because your background values are so high. >> On Thu, 15 Feb >> 2007, Anil Roy wrote: >> >> > Thanks a lot Nick. >> > >> > I'll try to convert the AFNI skull strip into brainmask and
nu
and
see >> if I >> > can resume the pipeline. >> > >> > I put in the new values for the xfm and ran recon-all again
with
the
>> > notalairach flag. >> > >> > recon-all -s Nl-TAl-001 -notalairach -all >> > >> > However, it still quits at the watershed step. I ran another
brain
where >> the >> > raw images were dcm and it ran fine so the problem is
definitely
>> something >> > specific to this brain. >> > >> > Nick, I know that autorecon1 ran fine for you so I really
have
no
clue >> why >> > my machine quits at the watershed step even with the
transform
you
gave >> me. >> > >> > Any clues, suggestions? >> > >> > Thanks a lot, >> > >> > Anil. >> > >> > On 2/14/07, Nick Schmansky < nicks@nmr.mgh.harvard.edu>
wrote:
>> >> >> >> Anil, >> >> >> >> Here is the transform (the contents of the talairach.xfmfile)
that
I >> >> generated: >> >> >> >> Transform_Type = Linear; >> >> Linear_Transform = >> >> 9.265516e-01 5.678305e-04 2.317888e-03 3.736965e-01 >> >> -8.173273e-04 8.513330e-01 8.824052e-02 -1.653205e+01 >> >> - 2.688466e-03 -1.064786e-01 9.460568e-01 1.780552e+01 ; >> >> >> >> Remember to use the -notalairach flag with recon-all when
you
create
>> the >> >> new talairach.xfm file, so that it doesnt get overwritten. >> >> >> >> 4GB is plenty to run Freesurfer, so it is strange that
mri_watershed
is >> >> encountering out-of-memory errors. >> >> >> >> Nick >> >> >> >> >> >> On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote: >> >> > Also, I ran it on a Red Hat system and I'm still getting
the
error
so >> >> > I don't think it is a machine specific problem. Any
suggestions.
>> >> > >> >> > Thanks. >> >> > Anil. >> >> > >> >> > On 2/14/07, Anil Roy < aroy85@gmail.com> wrote: >> >> > Here are the details of the acquisitions: >> >> > >> >> > Images acquired on a 3T Signa scanner with a
standard
GE
head >> >> > coil. 3D T1-weighted spiral volume scan (120
slices,
>> 1.4875-mm >> >> > thick, TR = 20 msec, TE = 6 msec, 40 degrees flip
angle,
256 >> * >> >> > 192 matrix) >> >> > >> >> > The machine has 4 gigs of RAM. Also, AFNI is able
to
>> talairach >> >> > and skull strip. Is there a way I can input the
files
from
>> >> > AFNI to Freesurfer to resume the recon-all
pipeline.
>> >> > >> >> > Nick, is there a way for me to see your reg so
that I
can
be >> >> > sure that its not my created xfm that is causing
this
>> >> > problem. >> >> > >> >> > Thanks, >> >> > >> >> > Anil. >> >> > >> >> > >> >> > On 2/14/07, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote: >> >> > why is the background so high? Also, what
field
>> >> > strength was this at? There >> >> > looks to be dielectric-like center
brightening.
The >> >> > contrast isn't terrible >> >> > though. >> >> > >> >> > On Wed, 14 Feb 2007, Nick >> >> > Schmansky wrote: >> >> > >> >> > > Bruce, >> >> > > >> >> > > the orig.mgz can be downloaded via the
filedrop,
>> see >> >> > link in email >> >> > > below. >> >> > > >> >> > > or i have copied it to: >> >> > > >> >> > >> >> > /autofs/space/minerva_001/users/nicks/subjects/anil/mri >> >> > > >> >> > > N. >> >> > > >> >> > > >> >> > > On Wed, 2007-02-14 at 17:02 -0500, Bruce
Fischl
>> >> > wrote: >> >> > >> put the .mgz somewhere and I'll take a
look.
And >> >> > make sure it's the >> >> > >> orig.mgz, which is un-normalized >> >> > >> >> >> > >> >> >> > >> On Wed, 14 Feb 2007, Nick Schmansky
wrote:
>> >> > >> >> >> > >>> Anil, >> >> > >>> >> >> > >>> The image has almost no
contrast. I've
attached >> a >> >> > TIFF of one slice. >> >> > >>> How was this acquired? Bruce, any
idea
why it
>> >> > would be so white? >> >> > >>> >> >> > >>> Nick >> >> > >>> >> >> > >>> >> >> > >>> On Wed, 2007-02-14 at 16:10 -0500, >> >> > aroy85@gmail.com wrote: >> >> > >>>> The following files have been
uploaded
to the
>> >> > Martinos Center FileDrop site >> >> > >>>> by Anil Roy for you to download: >> >> > >>>> >> >> > >>>> (1) orig.mgz >> >> > >>>> >> >> > >>>> >> >> > >>>> >> >> > >>>> These files will expire in 30 days. >> >> > >>>> >> >> > >>>> To view or download these files, go
in
your
web >> >> > browser to: >> >> > >>>> >> >> > >>>> >> >> > >> >> >>
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc7...
>> >> > >>>> >> >> > >>>> DO NOT SHARE this web address with
anyone
>> >> > else. It is your personal access key to
the
files. >> >> > >>>> >> >> > >>>> Overall Comment about files from Anil
Roy:
>> >> > >>>> >> >> > >>>> Hi, >> >> > >>>> >> >> > >>>> Attached is the orig.mgz file for the
subject
>> >> > that quits at the watershed step. >> >> > >>>> >> >> > >>>> Thanks, >> >> > >>>> >> >> > >>>> Anil. >> >> > >>>> >> >> > >>>> >> >> > >>> >> >> > >> >> >> > >> >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> >> >> > >> >
what are the background in the 001.mgz? Sorry, I haven't had a chance to look at it
On Tue, 27 Feb 2007, Anil Roy wrote:
Hi Bruce,
I've been trying to improve the talairach xfm and try different things with afni, but so far nothing has worked out. The brain still crashes at the skull strip. I fed in the afni skull strip to resume the pipeline from autorecon2 but the segmentation was really bad, with the white matter surface not accurate.
Did you have any suggestions for the background values.
Any ideas.
Thanks,
Anil.
On 2/21/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Anil,
I got the email, but I'm out of town and won't get to it until next week Bruce On Wed, 21 Feb 2007, Anil Roy wrote:
I think my last email didn't get through. Bruce, I've uploaded the
001.mgz.
It should arrive in your mailbox. I can upload it again if there was any problem.
Thanks,
Anil.
On 2/20/07, Anil Roy aroy85@gmail.com wrote:
Its uploaded
On 2/20/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I need the 001.mgz On Tue, 20 Feb 2007, Anil Roy wrote:
Bruce, I had uploaded the orig.mgz for Nick. I think you should
find
the
link below. I can also upload the 001.mgz for you. There are no dicoms because the scan is from a GE scanner (120
slices,
details are below)and all the files are named as I.??? I could also upload these files for you.
Anil.
On 2/20/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu > wrote: > > I think it's something afni is doing, but I'm not sure. Did you
give
us
> the data before conversion (either the dicoms or the 001.mgz) > > On Tue, 20 Feb 2007, > Anil Roy wrote: > > > Hey Freesurfers, > > > > I fed freesurfer the brainmask.mgz generated by AFNI. autorecon2
and
> > autorecon3 ran fine with no errors but the resulting surfaces
are
not
> very > > accurate. > > > > Bruce, you mentioned that my background values were too high. Is
there a
> way > > to reduce them so that freesurfer can do the watershed without
any
> glitches. > > > > Thanks, > > > > Anil. > > > > On 2/15/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > >> > >> I think it's because your background values are so high. > >> On Thu, 15 Feb > >> 2007, Anil Roy wrote: > >> > >> > Thanks a lot Nick. > >> > > >> > I'll try to convert the AFNI skull strip into brainmask and
nu
and
> see > >> if I > >> > can resume the pipeline. > >> > > >> > I put in the new values for the xfm and ran recon-all again
with
the
> >> > notalairach flag. > >> > > >> > recon-all -s Nl-TAl-001 -notalairach -all > >> > > >> > However, it still quits at the watershed step. I ran another
brain
> where > >> the > >> > raw images were dcm and it ran fine so the problem is
definitely
> >> something > >> > specific to this brain. > >> > > >> > Nick, I know that autorecon1 ran fine for you so I really
have
no
> clue > >> why > >> > my machine quits at the watershed step even with the
transform
you
> gave > >> me. > >> > > >> > Any clues, suggestions? > >> > > >> > Thanks a lot, > >> > > >> > Anil. > >> > > >> > On 2/14/07, Nick Schmansky < nicks@nmr.mgh.harvard.edu>
wrote:
> >> >> > >> >> Anil, > >> >> > >> >> Here is the transform (the contents of the talairach.xfmfile)
that
> I > >> >> generated: > >> >> > >> >> Transform_Type = Linear; > >> >> Linear_Transform = > >> >> 9.265516e-01 5.678305e-04 2.317888e-03 3.736965e-01 > >> >> -8.173273e-04 8.513330e-01 8.824052e-02 -1.653205e+01 > >> >> - 2.688466e-03 -1.064786e-01 9.460568e-01 1.780552e+01 ; > >> >> > >> >> Remember to use the -notalairach flag with recon-all when
you
create
> > >> the > >> >> new talairach.xfm file, so that it doesnt get overwritten. > >> >> > >> >> 4GB is plenty to run Freesurfer, so it is strange that
mri_watershed
> is > >> >> encountering out-of-memory errors. > >> >> > >> >> Nick > >> >> > >> >> > >> >> On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote: > >> >> > Also, I ran it on a Red Hat system and I'm still getting
the
error
> so > >> >> > I don't think it is a machine specific problem. Any
suggestions.
> >> >> > > >> >> > Thanks. > >> >> > Anil. > >> >> > > >> >> > On 2/14/07, Anil Roy < aroy85@gmail.com> wrote: > >> >> > Here are the details of the acquisitions: > >> >> > > >> >> > Images acquired on a 3T Signa scanner with a
standard
GE
> head > >> >> > coil. 3D T1-weighted spiral volume scan (120
slices,
> >> 1.4875-mm > >> >> > thick, TR = 20 msec, TE = 6 msec, 40 degrees flip
angle,
> 256 > >> * > >> >> > 192 matrix) > >> >> > > >> >> > The machine has 4 gigs of RAM. Also, AFNI is able
to
> >> talairach > >> >> > and skull strip. Is there a way I can input the
files
from
> > >> >> > AFNI to Freesurfer to resume the recon-all
pipeline.
> >> >> > > >> >> > Nick, is there a way for me to see your reg so
that I
can
> be > >> >> > sure that its not my created xfm that is causing
this
> >> >> > problem. > >> >> > > >> >> > Thanks, > >> >> > > >> >> > Anil. > >> >> > > >> >> > > >> >> > On 2/14/07, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> wrote: > >> >> > why is the background so high? Also, what
field
> >> >> > strength was this at? There > >> >> > looks to be dielectric-like center
brightening.
> The > >> >> > contrast isn't terrible > >> >> > though. > >> >> > > >> >> > On Wed, 14 Feb 2007, Nick > >> >> > Schmansky wrote: > >> >> > > >> >> > > Bruce, > >> >> > > > >> >> > > the orig.mgz can be downloaded via the
filedrop,
> >> see > >> >> > link in email > >> >> > > below. > >> >> > > > >> >> > > or i have copied it to: > >> >> > > > >> >> > > >> >> > /autofs/space/minerva_001/users/nicks/subjects/anil/mri > >> >> > > > >> >> > > N. > >> >> > > > >> >> > > > >> >> > > On Wed, 2007-02-14 at 17:02 -0500, Bruce
Fischl
> >> >> > wrote: > >> >> > >> put the .mgz somewhere and I'll take a
look.
> And > >> >> > make sure it's the > >> >> > >> orig.mgz, which is un-normalized > >> >> > >> > >> >> > >> > >> >> > >> On Wed, 14 Feb 2007, Nick Schmansky
wrote:
> >> >> > >> > >> >> > >>> Anil, > >> >> > >>> > >> >> > >>> The image has almost no
contrast. I've
> attached > >> a > >> >> > TIFF of one slice. > >> >> > >>> How was this acquired? Bruce, any
idea
why it
> > >> >> > would be so white? > >> >> > >>> > >> >> > >>> Nick > >> >> > >>> > >> >> > >>> > >> >> > >>> On Wed, 2007-02-14 at 16:10 -0500, > >> >> > aroy85@gmail.com wrote: > >> >> > >>>> The following files have been
uploaded
to the
> >> >> > Martinos Center FileDrop site > >> >> > >>>> by Anil Roy for you to download: > >> >> > >>>> > >> >> > >>>> (1) orig.mgz > >> >> > >>>> > >> >> > >>>> > >> >> > >>>> > >> >> > >>>> These files will expire in 30 days. > >> >> > >>>> > >> >> > >>>> To view or download these files, go
in
your
> web > >> >> > browser to: > >> >> > >>>> > >> >> > >>>> > >> >> > > >> >> > >> >
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc7...
> > >> >> > >>>> > >> >> > >>>> DO NOT SHARE this web address with
anyone
> >> >> > else. It is your personal access key to
the
> files. > >> >> > >>>> > >> >> > >>>> Overall Comment about files from Anil
Roy:
> >> >> > >>>> > >> >> > >>>> Hi, > >> >> > >>>> > >> >> > >>>> Attached is the orig.mgz file for the
subject
> > >> >> > that quits at the watershed step. > >> >> > >>>> > >> >> > >>>> Thanks, > >> >> > >>>> > >> >> > >>>> Anil. > >> >> > >>>> > >> >> > >>>> > >> >> > >>> > >> >> > >> > >> >> > >> > >> >> > > > >> >> > > > >> >> > > > >> >> > > >> >> > > >> >> > > >> >> > _______________________________________________ > >> >> > Freesurfer mailing list > >> >> > Freesurfer@nmr.mgh.harvard.edu > >> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >> > >> >> > >> > > >> > > >
You had mentioned that the background values were too high which was probably causing the brain to crash at the skull strip. I don't fully understand anything more than that about the background or if you need some specific details. Here are the specifics of the scan details.
Images acquired on a 3T Signa scanner with a standard GE head coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix)
Anil.
On 2/27/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what are the background in the 001.mgz? Sorry, I haven't had a chance to look at it
On Tue, 27 Feb 2007, Anil Roy wrote:
Hi Bruce,
I've been trying to improve the talairach xfm and try different things
with
afni, but so far nothing has worked out. The brain still crashes at the skull strip. I fed in the afni skull strip to resume the pipeline from autorecon2 but the segmentation was really bad, with the white matter surface not accurate.
Did you have any suggestions for the background values.
Any ideas.
Thanks,
Anil.
On 2/21/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Anil,
I got the email, but I'm out of town and won't get to it until next
week
Bruce On Wed, 21 Feb 2007, Anil Roy wrote:
I think my last email didn't get through. Bruce, I've uploaded the
001.mgz.
It should arrive in your mailbox. I can upload it again if there was
any
problem.
Thanks,
Anil.
On 2/20/07, Anil Roy aroy85@gmail.com wrote:
Its uploaded
On 2/20/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I need the 001.mgz On Tue, 20 Feb 2007, Anil Roy wrote:
> Bruce, I had uploaded the orig.mgz for Nick. I think you should
find
the > link below. I can also upload the 001.mgz for you. > There are no dicoms because the scan is from a GE scanner (120
slices,
> details are below)and all the files are named as I.??? > I could also upload these files for you. > > Anil. > > On 2/20/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu > wrote: >> >> I think it's something afni is doing, but I'm not sure. Did you
give
us >> the data before conversion (either the dicoms or the 001.mgz) >> >> On Tue, 20 Feb 2007, >> Anil Roy wrote: >> >> > Hey Freesurfers, >> > >> > I fed freesurfer the brainmask.mgz generated by AFNI.
autorecon2
and >> > autorecon3 ran fine with no errors but the resulting surfaces
are
not >> very >> > accurate. >> > >> > Bruce, you mentioned that my background values were too high.
Is
there a >> way >> > to reduce them so that freesurfer can do the watershed
without
any
>> glitches. >> > >> > Thanks, >> > >> > Anil. >> > >> > On 2/15/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: >> >> >> >> I think it's because your background values are so high. >> >> On Thu, 15 Feb >> >> 2007, Anil Roy wrote: >> >> >> >> > Thanks a lot Nick. >> >> > >> >> > I'll try to convert the AFNI skull strip into brainmask
and
nu
and >> see >> >> if I >> >> > can resume the pipeline. >> >> > >> >> > I put in the new values for the xfm and ran recon-all
again
with
the >> >> > notalairach flag. >> >> > >> >> > recon-all -s Nl-TAl-001 -notalairach -all >> >> > >> >> > However, it still quits at the watershed step. I ran
another
brain >> where >> >> the >> >> > raw images were dcm and it ran fine so the problem is
definitely
>> >> something >> >> > specific to this brain. >> >> > >> >> > Nick, I know that autorecon1 ran fine for you so I really
have
no >> clue >> >> why >> >> > my machine quits at the watershed step even with the
transform
you >> gave >> >> me. >> >> > >> >> > Any clues, suggestions? >> >> > >> >> > Thanks a lot, >> >> > >> >> > Anil. >> >> > >> >> > On 2/14/07, Nick Schmansky < nicks@nmr.mgh.harvard.edu>
wrote:
>> >> >> >> >> >> Anil, >> >> >> >> >> >> Here is the transform (the contents of the
talairach.xfmfile)
that >> I >> >> >> generated: >> >> >> >> >> >> Transform_Type = Linear; >> >> >> Linear_Transform = >> >> >> 9.265516e-01 5.678305e-04 2.317888e-03 3.736965e-01 >> >> >> -8.173273e-04 8.513330e-01 8.824052e-02 -1.653205e+01 >> >> >> - 2.688466e-03 -1.064786e-01 9.460568e-01 1.780552e+01 ; >> >> >> >> >> >> Remember to use the -notalairach flag with recon-all when
you
create >> >> >> the >> >> >> new talairach.xfm file, so that it doesnt get
overwritten.
>> >> >> >> >> >> 4GB is plenty to run Freesurfer, so it is strange that mri_watershed >> is >> >> >> encountering out-of-memory errors. >> >> >> >> >> >> Nick >> >> >> >> >> >> >> >> >> On Wed, 2007-02-14 at 17:20 -0600, Anil Roy wrote: >> >> >> > Also, I ran it on a Red Hat system and I'm still
getting
the
error >> so >> >> >> > I don't think it is a machine specific problem. Any suggestions. >> >> >> > >> >> >> > Thanks. >> >> >> > Anil. >> >> >> > >> >> >> > On 2/14/07, Anil Roy < aroy85@gmail.com> wrote: >> >> >> > Here are the details of the acquisitions: >> >> >> > >> >> >> > Images acquired on a 3T Signa scanner with a
standard
GE >> head >> >> >> > coil. 3D T1-weighted spiral volume scan (120
slices,
>> >> 1.4875-mm >> >> >> > thick, TR = 20 msec, TE = 6 msec, 40 degrees
flip
angle, >> 256 >> >> * >> >> >> > 192 matrix) >> >> >> > >> >> >> > The machine has 4 gigs of RAM. Also, AFNI is
able
to
>> >> talairach >> >> >> > and skull strip. Is there a way I can input the
files
from >> >> >> >> > AFNI to Freesurfer to resume the recon-all
pipeline.
>> >> >> > >> >> >> > Nick, is there a way for me to see your reg so
that I
can >> be >> >> >> > sure that its not my created xfm that
is causing
this >> >> >> > problem. >> >> >> > >> >> >> > Thanks, >> >> >> > >> >> >> > Anil. >> >> >> > >> >> >> > >> >> >> > On 2/14/07, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
>> wrote: >> >> >> > why is the background so high? Also,
what
field >> >> >> > strength was this at? There >> >> >> > looks to be dielectric-like center brightening. >> The >> >> >> > contrast isn't terrible >> >> >> > though. >> >> >> > >> >> >> > On Wed, 14 Feb 2007, Nick >> >> >> > Schmansky wrote: >> >> >> > >> >> >> > > Bruce, >> >> >> > > >> >> >> > > the orig.mgz can be downloaded via
the
filedrop, >> >> see >> >> >> > link in email >> >> >> > > below. >> >> >> > > >> >> >> > > or i have copied it to: >> >> >> > > >> >> >> > >> >> >>
/autofs/space/minerva_001/users/nicks/subjects/anil/mri
>> >> >> > > >> >> >> > > N. >> >> >> > > >> >> >> > > >> >> >> > > On Wed, 2007-02-14 at 17:02 -0500,
Bruce
Fischl >> >> >> > wrote: >> >> >> > >> put the .mgz somewhere and I'll take
a
look. >> And >> >> >> > make sure it's the >> >> >> > >> orig.mgz, which is un-normalized >> >> >> > >> >> >> >> > >> >> >> >> > >> On Wed, 14 Feb 2007, Nick Schmansky
wrote:
>> >> >> > >> >> >> >> > >>> Anil, >> >> >> > >>> >> >> >> > >>> The image has almost no
contrast. I've
>> attached >> >> a >> >> >> > TIFF of one slice. >> >> >> > >>> How was this acquired? Bruce, any
idea
why it >> >> >> >> > would be so white? >> >> >> > >>> >> >> >> > >>> Nick >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> On Wed, 2007-02-14 at 16:10 -0500, >> >> >> > aroy85@gmail.com wrote: >> >> >> > >>>> The following files have been
uploaded
to the >> >> >> > Martinos Center FileDrop site >> >> >> > >>>> by Anil Roy for you to download: >> >> >> > >>>> >> >> >> > >>>> (1) orig.mgz >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> These files will expire in 30
days.
>> >> >> > >>>> >> >> >> > >>>> To view or download these files,
go
in
your >> web >> >> >> > browser to: >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >> >> >> >> >> >>
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc7...
>> >> >> >> > >>>> >> >> >> > >>>> DO NOT SHARE this web address with anyone >> >> >> > else. It is your personal access key
to
the
>> files. >> >> >> > >>>> >> >> >> > >>>> Overall Comment about files from
Anil
Roy: >> >> >> > >>>> >> >> >> > >>>> Hi, >> >> >> > >>>> >> >> >> > >>>> Attached is the orig.mgz file for
the
subject >> >> >> >> > that quits at the watershed step. >> >> >> > >>>> >> >> >> > >>>> Thanks, >> >> >> > >>>> >> >> >> > >>>> Anil. >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>> >> >> >> > >> >> >> >> > >> >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > >> >> >> > >> >> >> > >> >> >> > _______________________________________________ >> >> >> > Freesurfer mailing list >> >> >> > Freesurfer@nmr.mgh.harvard.edu >> >> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> >> >> >> >> >> > >> >> >> > >> >
freesurfer@nmr.mgh.harvard.edu
-
Anil Roy -
Bruce Fischl