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
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