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