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.sharma1...@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.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
>>> >
>>> >
>>> >_______________________________________________
>>> 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
>
--
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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