Also, quick question . . .
How exactly do you run a recon from scratch without nifti images? I’d always delete the directory and restart with mri_convert -i …
Jon On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, I see the area you are talking about. I'm rerunning the recon from scratch to start with a clean copy since the case you sent has been rerun multiple times and there are a bunch of control points. The fact that the rh.orig.nofix looks good makes me optimistic that this can be fixed.
I'll get back to you soon. -Louis
On Mon, 4 Nov 2013, Louis Nicholas Vinke wrote:
Got it, I'll take a look.
On Mon, 4 Nov 2013, Jonathan Holt wrote:
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
maybe you should upload your data and we'll take a look
cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote:
Bruce,
If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I?m still confused after your response.
Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
this is almost certainly due to a topological defect. Improving the segmentation quality can frequently reduce the # of defects and get rid of big ones, so if you find that the wm segmentation isn't as visually accurate as is usually the case, using expert opts to improve its quality may also get rid of the problem you are seeing
cheers Bruce
On Mon, 4 Nov 2013, Jonathan Holt wrote:
> Hey Louis, > > thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running > > recon-all -autorecon2-noaseg -subjid <SUBJID> > > that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains. > > Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked? > > I?m open for ideas. > > I should also note that this problem is not an issue in rh.orig.nofix > > (sorry about duplicate email, Louis) > > > On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: > >> Hi Jon, >> The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). >> -Louis >> >> On Thu, 31 Oct 2013, Jonathan Holt wrote: >> >>> HI experts, >>> >>> I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? >>> >>> Jon >>> _______________________________________________ >>> 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 >> >> >> 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. > > > _______________________________________________ > 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 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 Jon, You can use the -clean flag, or you can just delete all the directories in the subject's recon directory except the mri folder, and then delete everything in the mri folder leaving the orig folder which contains the 001.mgz which is equivalent to the nifiti volume(s) initially passed to recon-all. -Louis
On Tue, 5 Nov 2013, Jonathan Holt wrote:
Also, quick question . . .
How exactly do you run a recon from scratch without nifti images? I’d always delete the directory and restart with mri_convert -i …
Jon On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote:
Hi Jon, I see the area you are talking about. I'm rerunning the recon from scratch to start with a clean copy since the case you sent has been rerun multiple times and there are a bunch of control points. The fact that the rh.orig.nofix looks good makes me optimistic that this can be fixed.
I'll get back to you soon. -Louis
On Mon, 4 Nov 2013, Louis Nicholas Vinke wrote:
Got it, I'll take a look.
On Mon, 4 Nov 2013, Jonathan Holt wrote:
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
maybe you should upload your data and we'll take a look
cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote:
Bruce,
If I understand you correctly, you?re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I?m still confused after your response.
Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
> Hi Jon > > this is almost certainly due to a topological defect. Improving the > segmentation quality can frequently reduce the # of defects and get rid of > big ones, so if you find that the wm segmentation isn't as visually > accurate as is usually the case, using expert opts to improve its quality > may also get rid of the problem you are seeing > > cheers > Bruce > > > > On Mon, 4 Nov 2013, Jonathan Holt wrote: > >> Hey Louis, >> >> thanks for your response. It?s actually a bit different, in my case an entire sulcus, including the empty space within it has been segmented and surfaced as white matter. I?m trying to reduce the WM surface such that the empty space is not included. I?ve tried removing segmentation manually and running >> >> recon-all -autorecon2-noaseg -subjid <SUBJID> >> >> that doesn?t work, the empty space is simply resegmented and the surface doesn?t change.. I should note that this has worked for me in the past on some brains. >> >> Since there are no WM voxels to remove I didn?t bother with removing any of them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t worked? >> >> I?m open for ideas. >> >> I should also note that this problem is not an issue in rh.orig.nofix >> >> (sorry about duplicate email, Louis) >> >> >> On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: >> >>> Hi Jon, >>> The limit numbers correspond to voxel intensities in the brainmask.mgz. I believe you will want a lower number for the -wlo/-wm_low flag to make the wm surf extend further out, assuming that the wm voxels that are not being captured by the surface is hypo-intense (<< 110). >>> -Louis >>> >>> On Thu, 31 Oct 2013, Jonathan Holt wrote: >>> >>>> HI experts, >>>> >>>> I?m wondering how these limits work, and whether the limit numbers indicate voxel intensity. If I wanted WM to be segmented more aggressively would I plug in a higher number or a lower number? >>>> >>>> Jon >>>> _______________________________________________ >>>> 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 >>> >>> >>> 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. >> >> >> _______________________________________________ >> 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 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@nmr.mgh.harvard.edu
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Louis Nicholas Vinke