External Email - Use Caution I'm trying to run this code but it's not working. What should be $i in the code? On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> or you could do that all on a single line: > > recon-all -i $SUBJECTS_DIR/$i/<nii or dcm file> -s $i -all > > cheers > Bruce > > On Mon, 19 Nov 2018, > Alex Hanganu > wrote: > > > > > 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 > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015
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