External Email - Use Caution I have a folder, lets name xyz which contains .nii file. Now I want to run recon-all for all the files in that folder. Please let me know how I can do that.
On Tue, Nov 20, 2018 at 11:40 AM Vivek Sharma <vivek.sharma1...@gmail.com> wrote: > 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 > -- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015
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