On Mon, Mar 25, 2019 at 7:15 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

yes, you don't need to process them separately. We don't in general
process slices - we process entire volumes

cheers
Bruce
On Mon, 25 Mar 2019, Chhavi Yadav
wrote:

>
>         External Email - Use Caution
>
> I meant I want to run autorecon1 over all the slices. I am trying to preprocess all the slices." If
> the rest of the dicoms are in the same dir we
> will find them and properly assemble the volume from them." means I dont have to preprocess all the
> slices separately? How do I get the preprocessed mgzs of all the rest of the slices?
>
> On Mon, Mar 25, 2019 at 7:08 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Hi Chhavi
>
> can you post this type of question to the FS list (which I'll cc on my
> response)? You only need to give recon-all a single dicom slice that is
> from the correct series. If the rest of the dicoms are in the same dir we
> will find them and properly assemble the volume from them.
>
> cheers
> Bruce
>
>
> On Mon, 25 Mar 2019, Chhavi Yadav wrote:
>
> >
> >         External Email - Use Caution
> >
> > Hi Bruce, is there a way I can do recon-all -autorecon1 for all the slices for a
> subject without
> > using the -i flag? I mean I do not want to mention every single slice's name in the
> command.
> >
> > On Mon, Mar 25, 2019 at 12:59 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> >
> > On Mon, 25 Mar 2019, Chhavi Yadav wrote:
> >
> > >
> > >         External Email - Use Caution
> > >
> > > Okay got it. So I will still writerecon-all -autorecon1 -i new.dcm -s outnew
> > > Just that new.dcm should be in the folder with the other slices. Is that
> correct?
> > >
> > > Also some of my slices are noisy, just ears or completely black.
> > > Sorry for sending to the list.
> > >
> > > Thanks for your help..
> > > Chhavi
> > >
> > >
> > > On Mon, Mar 25, 2019 at 12:44 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> wrote:
> > > Hi Chhavi
> > >
> > > if you look in the recon-all.log file you will see the volume dimensions
> > > as:
> > >
> > > Image information
> > >    RunNo 4
> > >    SeriesNo 5
> > >    ImageNo 56
> > >    NImageRows 256
> > >    NImageCols 240
> > >    NFrames 1
> > >    SliceArraylSize 1
> > >    IsMosaic 0
> > >    ImgPos 36.2753 164.5335 99.2486
> > >    VolRes 1.0000 1.0000 1.2000
> > >    VolDim 240 256 1
> > >    Vc -0.0000 -1.0000 0.0000
> > >    Vr -0.0000 -0.0000 -1.0000
> > >    Vs -1.0000 -0.0000 0.0000
> > >    VolCenter 35.6753 44.5335 -28.7514
> > >    TransferSyntaxUID 1.2.840.10008.1.2.1
> > >
> > >
> > > so it is only a single slice. You need to have the entire dicom series
> in
> > > the same directory so that we can find the other slices
> > > cheers
> > > Bruce
> > >
> > >
> > > On Mon, 25 Mar 2019,
> > > Chhavi Yadav wrote:
> > >
> > > >
> > > >         External Email - Use Caution
> > > >
> > > > attached is a sample on which it fails.I just do recon-all -autorecon1
> -i
> > new.dcm -s outnew
> > > >
> > > > Is this okay? Also attached is the log.
> > > > I haven't tried all.
> > > >
> > > > On Mon, Mar 25, 2019 at 12:26 PM Bruce Fischl
> <fischl@nmr.mgh.harvard.edu>
> > wrote:
> > > > did all of them fail? That seems unlikely. Our failure rates are
> usually
> > > > pretty low (less than a couple of percent). If they are all
> failing
> > > > something else is wrong
> > > >
> > > >
> > > > On Mon, 25 Mar 2019, Chhavi Yadav wrote:
> > > >
> > > > >
> > > > >         External Email - Use Caution
> > > > >
> > > > > HI Bruce,Thanks for your email.
> > > > > I actually have 3500 files. So cant do transform on them
> manually. Any
> > other way?
> > > Like
> > > > downloading the
> > > > > previous version of freesurfer?
> > > > > Chhavi
> > > > >
> > > > > On Mon, Mar 25, 2019 at 10:56 AM Bruce Fischl
> > <fischl@nmr.mgh.harvard.edu> wrote:
> > > > > Hi Chhavi
> > > > >
> > > > > the automated Talairach transform creation can sometimes
> fail,
> > > > > particularly in the presence of very large ventricles or
> lots of
> > > > > damaged white matter or
> > > > > both. We have a tutorial on checking and correcting it
> here:
> > > > >
> > > >    >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FsTutori
> a
> > l_Tala
> > > ir
> > > >
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> > HktL7Q
> > > rJ
> > > >
> > > > >
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> > > > >
> > > > > cheers
> > > > > Bruce
> > > > >
> > > > > On
> > > > > Mon, 25 Mar 2019, Chhavi Yadav wrote:
> > > > >
> > > > > >
> > > > > >         External Email - Use Caution
> > > > > >
> > > > > > Hi,I am a beginner to freesurfer. Never used it
> before.
> > > > > > Currently I am working on some dicoms from ADNI that I
> want to
> > preprocess.
> > > > > > But I am getting this 'talairach_afd: Talairach
> Transform:
> > > transforms/talairach.xfm
> > > > > ***FAILED*** ' error.
> > > > > > I am attaching the error log and other files for your
> > reference. Please
> > > help me
> > > > out.
> > > > > >
> > > > > > Regards,
> > > > > > Chhavi
> > > > > >
> > > > > >_______________________________________________
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> > > > >
> > > > >
> > > > >_______________________________________________
> > > > Freesurfer mailing list
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> > >    >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_f
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> > > >
> > > >
> > > >_______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> >   >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_fr
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