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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 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.
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.sharma1510@gmail.com a écrit :
External Email - Use CautionHi, 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
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.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.
-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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.
-- 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
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.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.
-- 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
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 $i -all -qcache done
subs.txt contains the name of folder that contains .nii file. The scripts ends with the following error:
ERROR: no run data found in /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to have a volume called 001.mgz in /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Please let me know how I can run recon-all for multiple subjects. Thank you.
-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015
-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015
in csh it would be something like
setenv SUBJECTS_DIR <whereever you want it> foreach fname ($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.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 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.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 $i -all -qcache > done > > subs.txt contains the name of folder that contains .nii file. > The scripts ends with the following error: > > ERROR: no run data found in > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to > have a volume called 001.mgz in > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig. > If you have a second run of data call it 002.mgz, etc. > See also: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > Please let me know how I can run recon-all for multiple subjects. > Thank you. > > -- > Vivek Sharma > Mobile: +919953582034 > Skype: vivek.sharma1015 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015
-- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015
External Email - Use Caution
Thanks!
On Tue, Nov 20, 2018 at 8:57 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
in csh it would be something like
setenv SUBJECTS_DIR <whereever you want it> foreach fname ($dir/*.nii) set fonly=${f:t} set fnoext=${f:r} recon-all -i $fname -s $fnoext -all end
On Tue, 20 Nov 2018, Vivek Sharma wrote:
External Email - Use CautionI have a folder, lets name xyz which contains .nii file. Now I want to
run recon-all for all the
files in that folder. Please let me know how I can do that.
On Tue, Nov 20, 2018 at 11:40 AM Vivek Sharma <
vivek.sharma1510@gmail.com> wrote:
I'm trying to run this code but it's not working. What should be$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 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.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, butunable
> 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. Makesure 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
oh, that was from your example. -i <input file> should be the full path to the input volume *or* one file in the correct dicom series. -s <subject id> is something you choose to uniquely identify that subject's recon-all outputs
cheers Bruce
On Tue, 20 Nov 2018, Vivek Sharma wrote:
External Email - Use Caution
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 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.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. > > -- > 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
freesurfer@nmr.mgh.harvard.edu
-
Alex Hanganu -
Bruce Fischl -
Vivek Sharma