New subject: Files uploaded for you on Martinos Center FileDrop site

15 Feb 2007


      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

Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site