External Email - Use Caution
Thanks!
On Tue, Nov 20, 2018 at 8:57 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
>
> 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.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
> >
> >_______________________________________________
> 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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