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 CautionHi 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 -inew.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 thevolume 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 entiredicom 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 dorecon-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. Ourfailure rates are usually
> > pretty low (less than a couple of percent). Ifthey 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 transformon 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 creationcan sometimes fail,
> > > particularly in the presence of very largeventricles or lots of
> > > damaged white matter or > > > both. We have a tutorial on checking andcorrecting it here:
> > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
l_Tala > ir > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKb HktL7Q > rJ > > > > >
JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e=
> > > > > > cheers > > > Bruce > > > > > > On > > > Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > Hi,I am a beginner to freesurfer. Neverused it before.
> > > > Currently I am working on some dicomsfrom 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 otherfiles for your
reference. Please > help me > > out. > > > > > > > > Regards, > > > > Chhavi > > > > > > >
> > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
reesur > fe > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPu LToS-_ > 5l > > > > >
kY&s=bKPWvTI6mhmqTDXPcjuZiBrd9LczeJVcqb47rKN8Lvg&e=
> > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
eesurfe > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF_ c8g2VP7 > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
surfer&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1S2 TCg3F > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > >