woops- sorry meant to include everyone. The name of the file I use to plot is "lh.pial-outer-smoothed." So I either want to create this file or figure out another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 11, 2014 10:51 AM To: Borzello, Mia Subject: Re: [Freesurfer] creating specific files
Hi Mia
can you keep ccing the list? I don't know what the "outer smoothed pial surface" is. Is this something we create? I don't think so Bruce
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Plotting the electrodes on the surface using matlab. I usually use the
outer smoothed pial surface- do I first need the normal pial surface to create this? >
On Feb 11, 2014, at 10:42 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
what kind of plotting do you mean?
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Okay and is there a way to check if the files I currently have are sufficient to plot with?
Thanks, m
On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
if they are zero length there is nothing there now
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Is this okay to do even if I've done a coregistration, nothing will be deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if I can just use the files that I have to create a plot without having to rerun anything.
Thanks, Mia
On Feb 10, 2014, at 4:31 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Mia
delete the 0 length files and run recon-all -make all -s <subject>
cheers Bruce > On Mon, 10 Feb 2014, Borzello, Mia wrote: > > Hi Freesurfers, > I was wondering if there was a way to kind of fill in the blanks for a > Surfer Output folder. I am working with an old data set, and it seem that > some of the files are empty (0 bytes), "rh.pial" for example. Is there a way > to pass the SurferOutput folder in and recreate what's missing? > Thanks, > Mia
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
Another question- will I need to re-coregister if I rerun a reconstruction?
Thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Tuesday, February 11, 2014 11:05 AM To: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating specific files
woops- sorry meant to include everyone. The name of the file I use to plot is "lh.pial-outer-smoothed." So I either want to create this file or figure out another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 11, 2014 10:51 AM To: Borzello, Mia Subject: Re: [Freesurfer] creating specific files
Hi Mia
can you keep ccing the list? I don't know what the "outer smoothed pial surface" is. Is this something we create? I don't think so Bruce
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Plotting the electrodes on the surface using matlab. I usually use the
outer smoothed pial surface- do I first need the normal pial surface to create this? >
On Feb 11, 2014, at 10:42 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
what kind of plotting do you mean?
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Okay and is there a way to check if the files I currently have are sufficient to plot with?
Thanks, m
On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
if they are zero length there is nothing there now
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Is this okay to do even if I've done a coregistration, nothing will be deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if I can just use the files that I have to create a plot without having to rerun anything.
Thanks, Mia
On Feb 10, 2014, at 4:31 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Mia
delete the 0 length files and run recon-all -make all -s <subject>
cheers Bruce > On Mon, 10 Feb 2014, Borzello, Mia wrote: > > Hi Freesurfers, > I was wondering if there was a way to kind of fill in the blanks for a > Surfer Output folder. I am working with an old data set, and it seem that > some of the files are empty (0 bytes), "rh.pial" for example. Is there a way > to pass the SurferOutput folder in and recreate what's missing? > Thanks, > Mia
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you shouldn't On Tue, 11 Feb 2014, Borzello, Mia wrote:
Another question- will I need to re-coregister if I rerun a reconstruction?
Thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Tuesday, February 11, 2014 11:05 AM To: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating specific files
woops- sorry meant to include everyone. The name of the file I use to plot is "lh.pial-outer-smoothed." So I either want to create this file or figure out another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 11, 2014 10:51 AM To: Borzello, Mia Subject: Re: [Freesurfer] creating specific files
Hi Mia
can you keep ccing the list? I don't know what the "outer smoothed pial surface" is. Is this something we create? I don't think so Bruce
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Plotting the electrodes on the surface using matlab. I usually use the
outer smoothed pial surface- do I first need the normal pial surface to create this? >
On Feb 11, 2014, at 10:42 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
what kind of plotting do you mean?
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Okay and is there a way to check if the files I currently have are sufficient to plot with?
Thanks, m
On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
if they are zero length there is nothing there now
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Is this okay to do even if I've done a coregistration, nothing will be deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if I can just use the files that I have to create a plot without having to rerun anything.
Thanks, Mia
> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: > > Hi Mia > > delete the 0 length files and run recon-all -make all -s <subject> > > cheers > Bruce >> On Mon, 10 Feb 2014, Borzello, Mia wrote: >> >> Hi Freesurfers, >> I was wondering if there was a way to kind of fill in the blanks for a >> Surfer Output folder. I am working with an old data set, and it seem that >> some of the files are empty (0 bytes), "rh.pial" for example. Is there a way >> to pass the SurferOutput folder in and recreate what's missing? >> Thanks, >> Mia
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Mia
I don't know where that file comes from - I don't think it's one we typically generate, but I would imagine it does need the ?h.pial surface as input
cheers Bruce
On Tue, 11 Feb 2014, Borzello, Mia wrote:
woops- sorry meant to include everyone. The name of the file I use to plot is "lh.pial-outer-smoothed." So I either want to create this file or figure out another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 11, 2014 10:51 AM To: Borzello, Mia Subject: Re: [Freesurfer] creating specific files
Hi Mia
can you keep ccing the list? I don't know what the "outer smoothed pial surface" is. Is this something we create? I don't think so Bruce
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Plotting the electrodes on the surface using matlab. I usually use the
outer smoothed pial surface- do I first need the normal pial surface to create this? >
On Feb 11, 2014, at 10:42 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
what kind of plotting do you mean?
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Okay and is there a way to check if the files I currently have are sufficient to plot with?
Thanks, m
On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
if they are zero length there is nothing there now
On Tue, 11 Feb 2014, Borzello, Mia wrote:
Is this okay to do even if I've done a coregistration, nothing will be deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if I can just use the files that I have to create a plot without having to rerun anything.
Thanks, Mia
> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: > > Hi Mia > > delete the 0 length files and run recon-all -make all -s <subject> > > cheers > Bruce >> On Mon, 10 Feb 2014, Borzello, Mia wrote: >> >> Hi Freesurfers, >> I was wondering if there was a way to kind of fill in the blanks for a >> Surfer Output folder. I am working with an old data set, and it seem that >> some of the files are empty (0 bytes), "rh.pial" for example. Is there a way >> to pass the SurferOutput folder in and recreate what's missing? >> Thanks, >> Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Borzello, Mia -
Bruce Fischl