On 2/27/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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 fed in the afni skull strip to resume the pipeline from
> autorecon2 but the segmentation was really bad, with the white matter
> surface not accurate.
>
> Did you have any suggestions for the background values.
>
> Any ideas.
>
> Thanks,
>
> Anil.
>
> 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.xfmfile )
>> >> > 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
>> >> > >> >> >>
>> >> > >> >> >>
>> >> > >> >> >
>> >> > >> >>
>> >> > >> >
>> >> > >>
>> >> > >
>> >> >
>> >>
>> >>
>> >
>>
>