External Email - Use Caution
Okay but then how do I access the mgzs of the rest of the slices? since only one folder was formed which I suppose has the output for a single slice which was mentioned in the recon-all command with -i flag.
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 CautionI 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 ccon my
response)? You only need to give recon-all a single dicom slicethat is
from the correct series. If the rest of the dicoms are in the samedir 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 allthe slices for a
subject without > using the -i flag? I mean I do not want to mention every singleslice'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 otherslices. Is that
correct? > > > > Also some of my slices are noisy, just ears orcompletely 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 seethe volume dimensions
> > as: > > > > Image information > > RunNo 4 > > SeriesNo 5 > > ImageNo 56 > > NImageRows 256 > > NImageCols 240 > > NFrames 1 > > SliceArraylSize 1 > > IsMosaic 0 > > ImgPos 36.2753 164.533599.2486
> > VolRes 1.0000 1.00001.2000
> > VolDim 240 256 1 > > Vc -0.0000 -1.00000.0000
> > Vr -0.0000 -0.0000-1.0000
> > Vs -1.0000 -0.00000.0000
> > 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 theentire dicom series
in > > the same directory so that we can find the otherslices
> > 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.Our failure rates are
usually > > > pretty low (less than a couple ofpercent). If they are all
failing > > > something else is wrong > > > > > > > > > On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > HI Bruce,Thanks for your email. > > > > I actually have 3500 files. So cant dotransform on them
manually. Any > other way? > > Like > > > downloading the > > > > previous version of freesurfer? > > > > Chhavi > > > > > > > > On Mon, Mar 25, 2019 at 10:56 AM BruceFischl
> <fischl@nmr.mgh.harvard.edu> wrote: > > > > Hi Chhavi > > > > > > > > the automated Talairach transformcreation can sometimes
fail, > > > > particularly in the presence ofvery large ventricles or
lots of > > > > damaged white matter or > > > > both. We have a tutorial onchecking and correcting it
here: > > > > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
a > l_Tala > > ir > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDK
b > HktL7Q > > rJ > > > > > > > JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e= > > > > > > > > cheers > > > > Bruce > > > > > > > > On > > > > Mon, 25 Mar 2019, Chhavi Yadavwrote:
> > > > > > > > > > > > > > External Email - UseCaution
> > > > > > > > > > Hi,I am a beginner tofreesurfer. Never used it
before. > > > > > Currently I am working on somedicoms 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 andother files 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...
f > reesur > > fe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELP
u > 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...
r > 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...
ee > surfe >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1 S2 > TCg3F > > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > >