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 > _______________________________________________ > 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