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.xfm file) 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
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.xfm file) 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
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.xfm file) 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 totalairach
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
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.xfm file) 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 totalairach
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
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.xfm file) 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 GEhead
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 totalairach
and skull strip. Is there a way I can input the files fromAFNI to Freesurfer to resume the recon-all pipeline. Nick, is there a way for me to see your reg so that I canbe
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'veattached
a
TIFF of one slice. >>> How was this acquired? Bruce, any idea why itwould 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 yourweb
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 thefiles.
>>>> >>>> Overall Comment about files from Anil Roy: >>>> >>>> Hi, >>>> >>>> Attached is the orig.mgz file for the subjectthat quits at the watershed step. >>>> >>>> Thanks, >>>> >>>> Anil. >>>> >>>> >>> >> >> > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.xfm file) 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
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.xfm file)
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 > >
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.xfm file)
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 >> >> >
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