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
>> >> >> >
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>> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >>
>> >> >>
>> >> >
>> >>
>> >
>>
>