if you can skull strip them you should be able to run the stream
afterwards. I've never seen an image with the background so high though -
it's something you should try to fix on the acquisition end.
On Wed, 28 Feb
2007, Anil Roy wrote:
Yes, if I just run the raw files, then the brain crashes
Yes, if I just run the raw files, then the brain crashes so I don't get any
output. But the background values are high in the orig.mgz file also and the
xfm is not accurate.
afni however is able to process all these raw files without a problem
including the talairach and skull strip.
Is there so
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
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
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 matte
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 <[EMAIL PROTECTED]> wrote:
>
> Its uploaded
>
> On 2/20/07, Bruce Fischl < [EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> wrote:
Its uploaded
On 2/20/07, Bruce Fischl <[EMAIL PROTECTED]> wrote:
>
> I n
Its uploaded
On 2/20/07, Bruce Fischl <[EMAIL PROTECTED]> 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 fro
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
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.
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
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 wat
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
notalaira
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
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 <[EMAIL PROTECTED]> wrote:
Here are the details of the acquisitions:
Images acquired on a 3T Signa scanner with a standard
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 t
Anil,
I was able to successfully run -autorecon1 (after performing my own tal
alignment). This included the skullstrip.
How much memory does your machine have? It needs to have at least 2GB.
Nick
On Wed, 2007-02-14 at 15:49 -0600, Anil Roy wrote:
> Nick,
>
> The files were acquired axially(
Anil,
On this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
there is a TIFF image of some example scans having decent contrast.
Nick
On Wed, 2007-02-14 at 17:03 -0500, Bruce Fischl wrote:
> can you tell us the details of the acquisition? The contrast is
> intrinsic
can you tell us the details of the acquisition? The contrast is
intrinsic, and it has to be sufficient for g/w segmentation.
On Wed, 14 Feb
2007, Anil Roy wrote:
Nick,
The files were acquired axially(120 slices) on a GE scanner. These scans are
a couple of years old. I should also inform yo
Nick,
The files were acquired axially(120 slices) on a GE scanner. These scans are
a couple of years old. I should also inform you that I converted the orginal
120 slices into afni brik format (afni was able to read them) and then used
mri_convert to convert the BRIK to cor. Freesurfer then used
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