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. >>>> >>>> >>> >> >> > > >
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