in csh it would be something like

setenv SUBJECTS_DIR <whereever you want it>
foreach fname ($dir/*.nii)
        set fonly=${f:t}
        set fnoext=${f:r}
        recon-all -i $fname -s $fnoext -all
end


On Tue, 20 Nov 2018, Vivek Sharma wrote:

>
>         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.sharma1510@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 <fischl@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.sharma1510@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
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>       >
>       >
>       >_______________________________________________
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>
>
>
> --
> Vivek Sharma
> Mobile: +919953582034
> Skype: vivek.sharma1015
>
>
>
> --
> Vivek Sharma
> Mobile: +919953582034
> Skype: vivek.sharma1015
>
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