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.
>> >> > >>>>
>> >> > >>>>
>> >> > >>>
>> >> > >>
>> >> > >>
>> >> > >
>> >> > >
>> >> > >
>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
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>> >> >
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>> >> >
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>> >>
>> >>
>> >
>>
>