Hi FreeSurfer Team,
My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for -autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2-pial -autorecon3. This flag hasn't been successful in version 6, producing an error message that the flag is unrecognized. Because we still only require some brainmask edits on the longs, we would like to know how we can continue to run these to process only pial.
All help is greatly appreciated!
Allison
Hi Allison,
seems like autorecon2-pial has been removed from FreeSurfer (also in the cross sectional stream). I don't know when, why and what would be the equivalent command, but someone on the list will know.
About brainmask edits, they are described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
The brainmask in the base is the union of all mask from cross (after registration) and is fixed for all time points. If the mask is correct, this is usually OK. So it makes sense to edit the brainmask in the base and not in the individual time points. In the base you would re-run autorecon2 and autorecon3 as the edited brainmask affects not just the surfaces, but also aseg etc.
If edits are really needed in the long runs, then edit it there and also run autorecon2 and autorecon3.
Best, Martin
On 07/14/2017 07:28 PM, Allison Rainford wrote:
Hi FreeSurfer Team,
My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for –autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2–pial –autorecon3. This flag hasn’t been successful in version 6, producing an error message that the flag is unrecognized. Because we still only require some brainmask edits on the longs, we would like to know how we can continue to run these to process only pial.
All help is greatly appreciated!
Allison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin
I believe it has been replaced with -autorecon-pial (since some of the pial surface generation has moved to autorecon3)
cheers Bruce On Mon, 17 Jul 2017, Martin Reuter wrote:
Hi Allison,
seems like autorecon2-pial has been removed from FreeSurfer (also in the cross sectional stream). I don't know when, why and what would be the equivalent command, but someone on the list will know.
About brainmask edits, they are described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
The brainmask in the base is the union of all mask from cross (after registration) and is fixed for all time points. If the mask is correct, this is usually OK. So it makes sense to edit the brainmask in the base and not in the individual time points. In the base you would re-run autorecon2 and autorecon3 as the edited brainmask affects not just the surfaces, but also aseg etc.
If edits are really needed in the long runs, then edit it there and also run autorecon2 and autorecon3.
Best, Martin
On 07/14/2017 07:28 PM, Allison Rainford wrote: Hi FreeSurfer Team,
My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for –autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2–pial –autorecon3. This flag hasn’t been successful in version 6, producing an error message that the flag is unrecognized. Because we still only require some brainmask edits on the longs, we would like to know how we can continue to run these to process only pial.
All help is greatly appreciated!
Allison
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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Allison Rainford -
Bruce Fischl -
Martin Reuter