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
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
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
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
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
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
Hi Mia,
while that is possible, it may be smarter to re-run those subjects from scratch. It is unclear why those files are empty. Maybe there are files that have been partially written etc. Those would not be re-created. I'd be very reluctant re-using data even partially that I know has been corrupted somehow. When re-running use the same FS version that was used initially, or better re-run the whole dataset with 5.3 if the data is really old.
Best, Martin
On 02/10/2014 04:31 PM, Bruce Fischl 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@nmr.mgh.harvard.edu
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Borzello, Mia -
Bruce Fischl -
Martin Reuter