Dear Doug,
do you think that it is necessary/useful to rerun
-normalization2 -maskbfs -segmentation
steps after wm.mgz have been edited (that is what the -autorecon2-wm is used for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
In contrast, it seems to me that the documentation is more close to the optimum (the three steps: normalization, mask and segmentation steps are run only when it is needed - in -autorecon2-cp, not in -autorecon2-wm).
Antonin
I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote:
Dear experts,
I noticed inconsistency between recon-all -help and actual code of recon-all in -autorecon2-wm option. According to the recon-all --help the -autorecon2-wm processes stages 15-23 (fill through make white surfaces) and -autorecon2-cp processes stages 12-23 (normalization2 throuhgh make white surfaces). But, in the code both -autorecon2-wm and -autorecon2-cp are equivalently processing stages 12-23.
It seems to me that the stages 12-14 are not needed to process again in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
Could you please comment on?
Regards,
Antonin Skoch
I'm not sure. The problem is in the segmentation. There are several steps in the segmentation, and it actually gets it right in the early ones but then undoes it later on. There are some parameters that can be played with (eg, -prior 0.5), I just have not had the chance to dig into it.
On 04/10/2017 04:24 PM, Antonin Skoch wrote:
Dear Doug,
do you think that it is necessary/useful to rerun
-normalization2 -maskbfs -segmentation
steps after wm.mgz have been edited (that is what the -autorecon2-wm is used for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
In contrast, it seems to me that the documentation is more close to the optimum (the three steps: normalization, mask and segmentation steps are run only when it is needed - in -autorecon2-cp, not in -autorecon2-wm).
Antonin
I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote:
Dear experts,
I noticed inconsistency between recon-all -help and actual code of recon-all in -autorecon2-wm option. According to the recon-all --help the -autorecon2-wm processes stages 15-23 (fill through make white surfaces) and -autorecon2-cp processes stages 12-23 (normalization2 throuhgh make white surfaces). But, in the code both -autorecon2-wm and -autorecon2-cp are equivalently processing stages 12-23.
It seems to me that the stages 12-14 are not needed to process again in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
Could you please comment on?
Regards,
Antonin Skoch
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
oops, sorry, I thought you were asking about your other question...
On 04/10/2017 04:45 PM, Douglas N Greve wrote:
I'm not sure. The problem is in the segmentation. There are several steps in the segmentation, and it actually gets it right in the early ones but then undoes it later on. There are some parameters that can be played with (eg, -prior 0.5), I just have not had the chance to dig into it.
On 04/10/2017 04:24 PM, Antonin Skoch wrote:
Dear Doug,
do you think that it is necessary/useful to rerun
-normalization2 -maskbfs -segmentation
steps after wm.mgz have been edited (that is what the -autorecon2-wm is used for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
In contrast, it seems to me that the documentation is more close to the optimum (the three steps: normalization, mask and segmentation steps are run only when it is needed - in -autorecon2-cp, not in -autorecon2-wm).
Antonin
I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote:
Dear experts,
I noticed inconsistency between recon-all -help and actual code of recon-all in -autorecon2-wm option. According to the recon-all --help the -autorecon2-wm processes stages 15-23 (fill through make white surfaces) and -autorecon2-cp processes stages 12-23 (normalization2 throuhgh make white surfaces). But, in the code both -autorecon2-wm and -autorecon2-cp are equivalently processing stages 12-23.
It seems to me that the stages 12-14 are not needed to process again in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
Could you please comment on?
Regards,
Antonin Skoch
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
They are being run but do not need to be. It does not change the results, but it is not needed and wastes cycles.
On 04/10/2017 04:24 PM, Antonin Skoch wrote:
Dear Doug,
do you think that it is necessary/useful to rerun
-normalization2 -maskbfs -segmentation
steps after wm.mgz have been edited (that is what the -autorecon2-wm is used for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
In contrast, it seems to me that the documentation is more close to the optimum (the three steps: normalization, mask and segmentation steps are run only when it is needed - in -autorecon2-cp, not in -autorecon2-wm).
Antonin
I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote:
Dear experts,
I noticed inconsistency between recon-all -help and actual code of recon-all in -autorecon2-wm option. According to the recon-all --help the -autorecon2-wm processes stages 15-23 (fill through make white surfaces) and -autorecon2-cp processes stages 12-23 (normalization2 throuhgh make white surfaces). But, in the code both -autorecon2-wm and -autorecon2-cp are equivalently processing stages 12-23.
It seems to me that the stages 12-14 are not needed to process again in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
Could you please comment on?
Regards,
Antonin Skoch
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Antonin Skoch -
Douglas N Greve