Re: [Freesurfer] Editing pial surface
hi Lars-
perhaps you need to delete more voxels. make sure you're editting the
brain volume, and you can just run make_final_surfaces if you only
want to regenerate a new pial surface (takes [a lot] less time).
thanks,
brian
On Mon, 12 Sep 2005, Lars Tjelta Westlye wrote:
Dear all,
I am trying to edit the pial surface by editing/deleting voxels in the
brain volume within the pial surface ('labeled' as a part of cortex), but
clearly are parts of dura when manually inspected. When I rerun the last
automatic procedures (fix, make_final, morph), and check the pial surface,
nothing has appeared to have changed. The voxels I deleted are gone,
though the pial surface still looks the same.
How can I fix this without having to regenerate/reconstruct all my
subjects? (I have approx. 100). Any tip?
I am by the way using the Freesurfer version from june (?) 2005, and due
to time restrictions I am not considering changing to the latest version
for this project.
Thanks a lot!
Best wishes,
Lars Tjelta Westlye
University of Oslo
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brian t. quinn
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Re: [Freesurfer] Editing pial surface
better to do it from inside recon-all so as to get it's bookkeeping. Run
with -finalsurfs
doug
Brian T. Quinn wrote:
hi Lars-
perhaps you need to delete more voxels. make sure you're editting the
brain volume, and you can just run make_final_surfaces if you only
want to regenerate a new pial surface (takes [a lot] less time).
thanks,
brian
On Mon, 12 Sep 2005, Lars Tjelta Westlye wrote:
Dear all,
I am trying to edit the pial surface by editing/deleting voxels in the
brain volume within the pial surface ('labeled' as a part of cortex),
but
clearly are parts of dura when manually inspected. When I rerun the last
automatic procedures (fix, make_final, morph), and check the pial
surface,
nothing has appeared to have changed. The voxels I deleted are gone,
though the pial surface still looks the same.
How can I fix this without having to regenerate/reconstruct all my
subjects? (I have approx. 100). Any tip?
I am by the way using the Freesurfer version from june (?) 2005, and due
to time restrictions I am not considering changing to the latest version
for this project.
Thanks a lot!
Best wishes,
Lars Tjelta Westlye
University of Oslo
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Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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[Freesurfer] subcortical segmentation
To Bruce Fischl and List, I just wanted to know if the subcortical segmentation featurehas been released. Thanks, Bosky ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] subcortical segmentation
I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912-full.tar.gz did the subcortical segmentation. I've run it on a couplde of brains so far and it seems to be ok. Are there still some bugs with it? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite, sorry. We *really* don't want to release a version with major problems, so we've been going through everything repeatedly trying to catch everything. We're getting there. Bruce On Mon, 12 Sep 2005, Bosky Ravindranath wrote: To Bruce Fischl and List, I just wanted to know if the subcortical segmentation feature has been released. Thanks, Bosky ___ 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] subcortical segmentation
Hi Alex, that was a prerelease version. The subcortical stuff seems fine, but we have fixed a couple of small bugs in other things, so we are going to recommend that people rerun things with the new official release that we are hoping to be done with soon (note that rerunning won't involve any manual interactions). Bruce On Tue, 13 Sep 2005, Fornito, Alexander wrote: I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912-full.tar.gz did the subcortical segmentation. I've run it on a couplde of brains so far and it seems to be ok. Are there still some bugs with it? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite, sorry. We *really* don't want to release a version with major problems, so we've been going through everything repeatedly trying to catch everything. We're getting there. Bruce On Mon, 12 Sep 2005, Bosky Ravindranath wrote: To Bruce Fischl and List, I just wanted to know if the subcortical segmentation feature has been released. Thanks, Bosky ___ 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] subcortical segmentation
yes, but they will be kept when you rerun. On Tue, 13 Sep 2005, Fornito, Alexander wrote: Fair enough. If recon-all is run without the subcortical segmentation, do manual edits to the wm volumes (eg., filling in ventricles, basal ganglia, etc) need to be performed? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 6:59 AM To: Fornito, Alexander Cc: Bosky Ravindranath; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] subcortical segmentation Hi Alex, that was a prerelease version. The subcortical stuff seems fine, but we have fixed a couple of small bugs in other things, so we are going to recommend that people rerun things with the new official release that we are hoping to be done with soon (note that rerunning won't involve any manual interactions). Bruce On Tue, 13 Sep 2005, Fornito, Alexander wrote: I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912-full.tar.gz did the subcortical segmentation. I've run it on a couplde of brains so far and it seems to be ok. Are there still some bugs with it? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite, sorry. We *really* don't want to release a version with major problems, so we've been going through everything repeatedly trying to catch everything. We're getting there. Bruce On Mon, 12 Sep 2005, Bosky Ravindranath wrote: To Bruce Fischl and List, I just wanted to know if the subcortical segmentation feature has been released. Thanks, Bosky ___ 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] large radius
HI, I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488 x 2). I seem to be able to convert them to .mgz ok, but when I run mri_watershed I get an error saying main radius too high (output below). Any ideas as to what's happening? Thanks, Alex mri_watershed 1001670.mgz 1001670_brain.mgz The input file is 1001670.mgz The output file is 1001670_brain.mgz If this is incorrect, please exit quickly the program (Ctl-C) *WATERSHED** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=253 y=50 z=235 r=135 first estimation of the main basin volume: 10415397 voxels Error main radius too high ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
