On Tue, Feb 7, 2017 at 2:36 PM, Antonin Skoch <ansk@ikem.cz> 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_HOME variable properly set before running the script?
To check that, put 
echo $FREESURFER_HOME

to the beginning of the script.

Antonin

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 /........../folder) before
running the script. Thanks. The scripts is below

#!bin/bash
# FreeSurfer Pipeline (stages 1-31)
# Written By Paul

set -e

# Source FreeSurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

# Start Scripts
echo -e "\n START: FreeSurferEntirePipeline"

# Input Variables
SubjectID="$1"
SubjectDIR="$2"
T1wImage="$3" #T1 FreeSurfer Input
T2wImage="$4" #T2 FreeSurfer Input


recon-all -s $SubjectID -autorecon-all -i "$T1wImage"_T1.nii -T2
"$T2wImage"_T2.nii -T2pial -parallel -hires

echo -e "done"
Best,
Paul

On Tue, Feb 7, 2017 at 4:40 AM, Antonin Skoch <a...@ikem.cz> wrote:

> 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 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
> >
>

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