External Email - Use Caution
ok so after the recon-all command runs, in the output directory's mri folder, a file called brainmask.mgz is formed. I have been doing a freeview -v of this file which corresponds to the final skull stripped output for my input slice that I wanted. Now as per the information that you gave me, I should have a volume. This leads me to two questions. How do I access the volume, where is it in the folder ? And how to I get slices again from this volume because originally I had slices and slices is what my system will further deal with.
On Mon, Mar 25, 2019 at 7:20 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
there are no outputs for single slices, only for volumes. After we convert the dicom series everything is a volume from then on, no more single slices On Mon, 25 Mar 2019, Chhavi Yadav wrote:
External Email - Use CautionOkay 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 Caution > > I meant I want to run autorecon1 over all the slices. I amtrying 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 therest 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 (whichI'll cc on my
> response)? You only need to give recon-all a single dicomslice that is
> from the correct series. If the rest of the dicoms are inthe 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 -autorecon1for all the slices for
a > subject without > > using the -i flag? I mean I do not want to mention everysingle 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 withthe other slices. 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 youwill see the volume
dimensions > > > as: > > > > > > Image information > > > RunNo 4 > > > SeriesNo 5 > > > ImageNo 56 > > > NImageRows 256 > > > NImageCols 240 > > > NFrames 1 > > > SliceArraylSize 1 > > > IsMosaic 0 > > > ImgPos 36.2753164.5335 99.2486
> > > VolRes 1.00001.0000 1.2000
> > > VolDim 240 2561> > > Vc -0.0000-1.0000 0.0000
> > > Vr -0.0000-0.0000 -1.0000
> > > Vs -1.0000-0.0000 0.0000
> > > VolCenter 35.675344.5335 -28.7514
> > > TransferSyntaxUID1.2.840.10008.1.2.1
> > > > > > > > > so it is only a single slice. You need tohave the entire dicom
series > in > > > the same directory so that we can find theother slices
> > > cheers > > > Bruce > > > > > > > > > On Mon, 25 Mar 2019, > > > Chhavi Yadav wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > attached is a sample on which it fails.Ijust 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 BruceFischl
> <fischl@nmr.mgh.harvard.edu> > > wrote: > > > > did all of them fail? That seemsunlikely. 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 Yadavwrote:
> > > > > > > > > > > > > > External Email - UseCaution
> > > > > > > > > > HI Bruce,Thanks for your email. > > > > > I actually have 3500 files. Socant do transform on
them > manually. Any > > other way? > > > Like > > > > downloading the > > > > > previous version of freesurfer? > > > > > Chhavi > > > > > > > > > > On Mon, Mar 25, 2019 at 10:56 AMBruce Fischl
> > <fischl@nmr.mgh.harvard.edu> wrote: > > > > > Hi Chhavi > > > > > > > > > > the automated Talairachtransform creation can
sometimes > fail, > > > > > particularly in thepresence of very large
ventricles or > lots of > > > > > damaged white matter or > > > > > both. We have a tutorialon checking and
correcting it > here: > > > > > > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
ori > a > > l_Tala > > > ir > > > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVT
tDK > b > > HktL7Q > > > rJ > > > > > > > > > >JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e=
> > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > On > > > > > Mon, 25 Mar 2019, ChhaviYadav wrote:
> > > > > > > > > > > > > > > > > External Email -Use Caution
> > > > > > > > > > > > Hi,I am a beginner tofreesurfer. Never used
it > before. > > > > > > Currently I am workingon 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 errorlog and other 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...
fo_ > f > > reesur > > > fe > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJ
ELP > 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...
f > r > > eesurfe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20Ws
F > _ > > 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...
r > ee > > surfe > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv 1 > S2 > > TCg3F > > >
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> > > > > > > > > > > > > > > > > >