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
>
>
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--
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
--
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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