Hi Dorsa
can you just copy and paste the text into the email? It's much easier
than trying to look at images of text.
Your recon-all command finished successfully. Essentially you didn't tell
it to do anything except import the data and create the subject dir.
Typically you want to give the -all directive. I'm not sure what the
warnings are, but you can look at the subject's mri/orig/001.mgz volume in
freeview to see if it worked. Next time you give recon-all do it without
the -i (since it already imported the data) or it will complain
cheers
Bruce
On Tue, 28 Jun 2016, Dorsa Haji
Ghaffari wrote:
sure, following is the code I run:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/usr/local/freesurfer/subjects
recon-all -i LT7616_3TS_Copy_0001.dcm -subjid test3
And I have attached two screenshots of what I get after running the code.
On Tue, Jun 28, 2016 at 4:06 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Dorsa
you need to give us more information that that if you want us to
help you. Send us the full command line you ran and the full
screen output and log files for starters.
cheers
Bruce
On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:
Thank you! When I recon-all my files, I get the
following error:files are
not found to be different and cannot be sorted
Do you have any suggestions?
Thank you
Dorsa
On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
just give recon-all a single slice from the
series with -i
<slice file
name>. It will figure out
the rest of them
On Tue, 28 Jun 2016, Dorsa Haji Ghaffari
wrote:
> Hi,
> I am a little confused about how should I
save my files to
execute recon-all on
> them. I have 240 slices of dicom format and
I put them in a
folder in my
> subjects_dir. but I get errors when using
recon-all on the
folder containing the
> MRIs. Can you help me with that? I really
appreciate your help
>
> Thank you
>
> Dorsa
>
> On Mon, Jun 27, 2016 at 3:13 PM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
> Hi Dorsa
>
> what specific models do you need? The
10-20 hours is to
process the
> data
> from a single subject at a single
timepoint. If you
check out our
> wiki
>
(http://surfer.nmr.mgh.harvard.edu/fswiki) there
are
lots of
> tutorials and
> sample datasets and such
>
> cheers
> Bruce
>
> On Mon, 27 Jun 2016, Dorsa Haji
> Ghaffari wrote:
>
> > Hi,
> > I am graduate student at the
University of Michigan
and I am
> performing
> > research on deep brain stimulation.
I want to warp an
anatomical
> brain atlas
> > to individual patient MRIs to get
the patient specific
brain models
> out of
> > it. I chose FreeSurfer to do this
and I have installed
it on my
> computer. I
> > realized that it takes 10-20 hrs to
reconstruct the
image. I wanted
> to ask
> > if that is the time for one image?
or the whole series
of images?
> > I also wanted to ask if there is a
step by step
tutorial on how to
> do this.
> >
> > Thank you
> >
> > Dorsa Ghaffari
> >
> >
> >
> >
>
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The information in this e-mail is intended only for the person to whom it is
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