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Thanks!
On Tue, Nov 20, 2018 at 8:57 PM Bruce Fischl
wrote:
>
> in csh it would be something like
>
> setenv SUBJECTS_DIR
> foreach fname ($dir/*.nii)
> set fonly=${f:t}
> set fnoext=${f:r}
> recon-all -i $fname -s $fnoext
in csh it would be something like
setenv SUBJECTS_DIR
foreach fname ($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:
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I have a folder, lets name
oh, that was from your example. -i should be the full path to
the input volume *or* one file in the correct dicom series. -s
is something you choose to uniquely identify that subject's recon-all
outputs
cheers
Bruce
On Tue, 20 Nov 2018, Vivek Sharma wrote:
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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
wrote:
> I have a folder, lets
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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
wrote:
> I'm trying to run this code but it's
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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
wrote:
> or you could do that all on a single line:
>
> recon-all -i $SUBJECTS_DIR/$i/ -s $i -all
>
> cheers
> Bruce
>
> On
or you could do that all on a single line:
recon-all -i $SUBJECTS_DIR/$i/ -s $i -all
cheers
Bruce
On Mon, 19 Nov 2018,
Alex Hanganu
wrote:
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HI Vivek,
you probably need 2 steps, first registration, second recon-all. Something
like:
...
do
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HI Vivek,
you probably need 2 steps, first registration, second recon-all. Something
like:
...
do
recon-all -i $SUBJECTS_DIR/$i/ -s $i
recon-all -all -subjid $i
I didn't check if the scrips runs. That's the general structure.
Best,
Alex
Le
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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
