On 2/21/07, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:

Hi Anil,

I got the email, but I'm out of town and won't get to it until next week
Bruce
On
Wed, 21 Feb 2007, Anil Roy 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 <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/5010/426/7389dc72a7ad03d19b7736c8a7adff69
>> >
>> > >>
>> > >> >> >> >                 >>>>
>> > >> >> >> >                 >>>> 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
>> > >> >> >>
>> > >> >> >>
>> > >> >> >
>> > >> >>
>> > >> >
>> > >>
>> > >
>> >
>>
>>
>