Do you know when the next version is slated to launch? That being said, if I wanted to salvage my work so far, is it best to just use the original "subcortical" output as is (if I was not trying to change it in the first place?).
-Mark Fletcher
On Wed, Oct 17, 2012 at 12:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Mark
it's hard to say if it's a "bug", but it is definitely a change in behavior that will go away with 5.2 (that is, we will no longer regenerate the aseg when you add control points).
cheers Bruce On Wed, 17 Oct 2012, Mark Fletcher wrote:
Dear FreeSurfers,
After adding WMCP to a number of my subjects (which corrected the
problem),
I retrieved to cortical and subcortical volumes from my subjects using
the
"aparcstats2table". I had used "aparcstats2table" before and after adding the control points. Accurately, the regions I wanted to change, did
change
in volume. However, the subcortical volumes post WMCP changed a lot as well? Some regions changed more than 20% after adding WMCP to other regions? Is this normal? Should I go with the original "subcortical" segmentation volumes, or the new ones? Is this part of the known bug in version 5.1.0 mentioned in the release notes about "running recon-all" a second time? Please advise?
Sincerely , Mark Fletcher
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I'm not really sure as I haven't done this much recently. Do you think the aseg results are less accurate after the cps? It's actually just a change in recon-all, so Nick could just post you an updated recon-all and you can rerun. Although you'll need to remove the control points, run recon-all, then rerun autorecon2-cp with the control points. You can save the control points by doing:
cd $SUBJECTS_DIR/$subject/tmp mv control.dat control.saved.dat
then when you want to restore them cd $SUBJECTS_DIR/$subject/tmp mv control.saved.dat control.dat
On Wed, 17 Oct 2012, Mark Fletcher wrote:
Do you know when the next version is slated to launch? That being said, if I wanted to salvage my work so far, is it best to just use the original "subcortical" output as is (if I was not trying to change it in the first place?).
-Mark Fletcher
On Wed, Oct 17, 2012 at 12:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mark
it's hard to say if it's a "bug", but it is definitely a change in behavior that will go away with 5.2 (that is, we will no longer regenerate the aseg when you add control points). cheers Bruce On Wed, 17 Oct 2012, Mark Fletcher wrote: > Dear FreeSurfers, > > After adding WMCP to a number of my subjects (which corrected the problem), > I retrieved to cortical and subcortical volumes from my subjects using the > "aparcstats2table". I had used "aparcstats2table" before and after adding > the control points. Accurately, the regions I wanted to change, did change > in volume. However, the subcortical volumes post WMCP changed a lot as > well? Some regions changed more than 20% after adding WMCP to other > regions? Is this normal? Should I go with the original "subcortical" > segmentation volumes, or the new ones? Is this part of the known bug in > version 5.1.0 mentioned in the release notes about "running recon-all" a > second time? Please advise? > > Sincerely , > Mark Fletcher > >The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Mark,
I've posted the recon-all that will be used in the upcoming v5.2, which contains the fix whereby control points are no longer used in the aseg, here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/
you can copy it to your v5.1 distro, but note i've named it recon-all-v5.2. if you rerun your subjects, use the flags:
-autorecon2 -autorecon3
Nick
On Wed, 2012-10-17 at 19:42 -0400, Bruce Fischl wrote:
I'm not really sure as I haven't done this much recently. Do you think the aseg results are less accurate after the cps? It's actually just a change in recon-all, so Nick could just post you an updated recon-all and you can rerun. Although you'll need to remove the control points, run recon-all, then rerun autorecon2-cp with the control points. You can save the control points by doing:
cd $SUBJECTS_DIR/$subject/tmp mv control.dat control.saved.dat
then when you want to restore them cd $SUBJECTS_DIR/$subject/tmp mv control.saved.dat control.dat
On Wed, 17 Oct 2012, Mark Fletcher wrote:
Do you know when the next version is slated to launch? That being said, if I wanted to salvage my work so far, is it best to just use the original "subcortical" output as is (if I was not trying to change it in the first place?).
-Mark Fletcher
On Wed, Oct 17, 2012 at 12:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mark
it's hard to say if it's a "bug", but it is definitely a change in behavior that will go away with 5.2 (that is, we will no longer regenerate the aseg when you add control points). cheers Bruce On Wed, 17 Oct 2012, Mark Fletcher wrote: > Dear FreeSurfers, > > After adding WMCP to a number of my subjects (which corrected the problem), > I retrieved to cortical and subcortical volumes from my subjects using the > "aparcstats2table". I had used "aparcstats2table" before and after adding > the control points. Accurately, the regions I wanted to change, did change > in volume. However, the subcortical volumes post WMCP changed a lot as > well? Some regions changed more than 20% after adding WMCP to other > regions? Is this normal? Should I go with the original "subcortical" > segmentation volumes, or the new ones? Is this part of the known bug in > version 5.1.0 mentioned in the release notes about "running recon-all" a > second time? Please advise? > > Sincerely , > Mark Fletcher > >The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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