External Email - Use Caution
Hi The following code worked. for asubject in /home/vivek/Downloads/freesurfer/subjects/*.nii; do recon-all -s ${asubject%.nii} -i $asubject -all -qcache; done
Thank you.
On Tue, Nov 20, 2018 at 12:19 PM Vivek Sharma vivek.sharma1510@gmail.com wrote:
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 CautionHI 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.
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-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015
-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015