Thank you very much Antonin. It worked.
Best,
Paul
On Tue, Feb 7, 2017 at 2:36 PM, Antonin Skoch wrote:
> Dear Paul,
>
> I don't know it it solves your problem, but if you are using bash shell, you
> have to source SetUpFreeSurfer.sh, not SetUpFreeSurfer.csh.
>
> And, do you have FREESURFER_HOM
Dear Paul,
I don't know it it solves your problem, but if you are using bash shell, you
have to source SetUpFreeSurfer.sh, not SetUpFreeSurfer.csh.
And, do you have FREESURFER_HOME variable properly set before running the
script?
To check that, put
echo $FREESURFER_HOME
to the beginning of th
Thanks Antonin and Bruce.
Also, I wrote a recon-all script and when I tried to run it, it gave me an
error (command not found). Please can anyone help me diagnosis what's wrong
with my scripts. I did set my subject directory to the current folder
(setenv SUBJECTS_DIR /../folder/; cd /.
Dear Paul,
maybe this is implicit, but to assure:
you have also to include -autorecon3.
Therefore the full command is:
recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial
Antonin
Yes, I think so
> On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
>
> Hello,
> I ran the entire
Yes, I think so
> On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
>
> Hello,
> I ran the entire recon pipeline with T2 option and then added control
> points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the
> pial surface or not? Thanks.
> Paul
>
> Sent from my B
Hello, I ran the entire recon pipeline with T2 option and then added control points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the pial surface or not? Thanks. Paul Sent from my BlackBerry 10 smartphone.
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