Re: [Freesurfer] How to automate recon-all command for multiple subjects
External Email - Use Caution
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 -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.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/ -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/ -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 $i -all -qcache
> > > done
> > >
> > > subs.txt contains the name of folder that contains .nii file.
> > > The scripts ends with the following error:
> > >
> > > ERROR: no run data found in
> > > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make
> sure to
> > > have a volume called 001.mgz in
> > > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
> > > If you have a second run of data call it 002.mgz, etc.
> > > See also:
> > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
> > > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
> > > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
> > >
> > > Please let me know how I can run recon-all for multiple subjects.
> > > Thank you.
> > >
> > > --
> > > Vivek Sharma
> > > Mobile: +919953582034
> > > Skype: vivek.sharma1015
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > --
> > Vivek Sharma
> > Mobile: +919953582034
> > Skype: vivek.sharma1015
> >
> >
> >
> > --
> > Vivek Sharma
> > Mobile: +919953582034
> > Skype: vivek.sharma1015
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to automate recon-all command for multiple subjects
in csh it would be something like
setenv SUBJECTS_DIR
foreach fname ($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:
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
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
wrote:
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:
>
> 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/ -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
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to automate recon-all command for multiple subjects
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: 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 wrote: 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: > > 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/ -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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to automate recon-all command for multiple subjects
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
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
> 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
>> wrote:
>>
>>> 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:
>>>
>>> >
>>> > 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/ -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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to automate recon-all command for multiple subjects
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 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 > wrote: > >> 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: >> >> > >> > 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/ -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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to automate recon-all command for multiple subjects
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 wrote: > 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: > > > > > 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/ -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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to automate recon-all command for multiple subjects
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: 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/ -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 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
Re: [Freesurfer] How to automate recon-all command for multiple subjects
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/ -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 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
[Freesurfer] How to automate recon-all command for multiple subjects
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
