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 ansk@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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