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 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
