you need to specify the SUBJECTS_DIR. And yes, you might have needed more
ram as the free is a lot less than the used at the start of recon-all, but
some clusters also have limits on the length of time a job is allowed to
run
cheers
Bruce
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
Do you mean that I should have used higher memory?
Is there a way to continue running it from where it stopped or should I start
it all over again?
On the Freesurfer Archive there's a suggestion to use the following command:
recon-all -make all -s
<subjid> However, when I tried it gave an error; ERROR: cannot find
/share/apps/freesurfer/6.0.0/subjects/103T.
On Thu, Aug 2, 2018 at 12:49 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
hmmm, it looks like it just stopped in the middle of a process. DId it
exceed some wall
time limit perhaps?
On Thu, 2 Aug 2018, Ortal Nakash wrote:
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Sure, here it is.
On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
can you send it as a text file (not converted to .docx)?
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
I copied it in the attached file.
Thank you,
Ortal
On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Ortal
you need to send us the recon-all.log, otherwise
we don't
have the
information we need
to help you
cheers
Bruce
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
Hi,
I tried to run the recon-all command on a
single
participant on
a high
memory cluster by typing:
qlogin -q qlogin.himem.q -l
h_vmem=20G,s_vmem=20G
recon-all -i 103_T1.nii.gz -s 103T -sd
/data/jag/cnds/ortal/freesurftest/C103/ -all
- Most of the necessary files were created,
however
the
aparc.a2009 files
and the recon-all.done
file were not.
sincerely,
Ortal Nakash
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