External Email - Use Caution HI Vivek,
you probably need 2 steps, first registration, second recon-all. Something like: ... do recon-all -i $SUBJECTS_DIR/$i/<nii or dcm file> -s $i recon-all -all -subjid $i I didn't check if the scrips runs. That's the general structure. Best, Alex Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma <vivek.sharma1...@gmail.com> a écrit : > External Email - Use Caution > > Hi, > I'm using freesurfer to generate head surfaces using MRI file. > I want to execute recon-all command for number of subjects, but unable to > run it. > The script I'm using is: > > for i in `cat *subs.txt*` > do > recon-all -s $i -all -qcache > done > > subs.txt contains the name of folder that contains .nii file. > The scripts ends with the following error: > > ERROR: no run data found in > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to > have a volume called 001.mgz in > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig. > If you have a second run of data call it 002.mgz, etc. > See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 > UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > Please let me know how I can run recon-all for multiple subjects. > Thank you. > > -- > Vivek Sharma > Mobile: +919953582034 > Skype: vivek.sharma1015 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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