Hi, I had been having a lot of trouble with the skull stripping in the newest dev version (it was taking off the top half of the head and leaving head and skull on the bottom half). I was able to fix this by redoing the intensity normalization step from autorecon1 using control points. My question is - In the brains where I did not have a problem with skull stripping, but after autorecon1 I have white matter intensity values below 110, should I redo intensity normalization with control points on them as well? Thanks! Kelli
Kelli,
In the newest dev version (Jan28 or Feb 10), certain defaults changed, which appear possibly not for the better. Could you try re-running recon-all on the failed subject, using flags which I'll describe in a second?
Attached is a new recon-all. To install, type this from where you have saved the attachment:
gunzip recon-all.gz chmod a+x recon-all cp recon-all $FREESURFER_HOME/bin/
Then, we'd first like you to try adding more iterations to the nu_correct step, as possibly your subject has large non-uniformities. Type the following (where <subject> is the name):
recon-all -s <subject> -autorecon1 -clean -nuiterations 4
This increases the iterations of the 'nu_correct' step from the default of 2 up to 4. See if the resulting skull strip is any better.
Note: the -clean flag will delete your control points! In fact, for now, please don't use control points! (not just yet anyway)
If the skull-strip still fails, try:
recon-all -s <subject> -autorecon1 -clean -no-wsatlas
The -no-wsatlas flag bypasses using an atlas during the skull-strip step (mri_watershed). We've had mixed results with using this atlas (mostly for the better), but its possible that it is the source of your troubles.
Lastly, you can try both flags:
recon-all -s <subject> -autorecon1 -clean -nuiterations 4 -no-wsatlas
If even this fails, then we may want to have a look at the subject files.
Thank you in advance for your patience!
Nick (and Xiao)
On Fri, 2006-02-10 at 16:49 -0500, dominick@bu.edu wrote:
Hi,
I had been having a lot of trouble with the skull stripping in the newest dev version (it was taking off the top half of the head and leaving head and skull on the bottom half). I was able to fix this by redoing the intensity normalization step from autorecon1 using control points. My question is - In the brains where I did not have a problem with skull stripping, but after autorecon1 I have white matter intensity values below 110, should I redo intensity normalization with control points on them as well?
Thanks!
Kelli
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
see if the ?h.white surface is accurate. If it is, then you're all set. If it's not then you can add a few control points in the dark wm in those regions.
cheers, Bruce On Fri, 10 Feb 2006 dominick@bu.edu wrote:
Hi, I had been having a lot of trouble with the skull stripping in the newest dev version (it was taking off the top half of the head and leaving head and skull on the bottom half). I was able to fix this by redoing the intensity normalization step from autorecon1 using control points. My question is - In the brains where I did not have a problem with skull stripping, but after autorecon1 I have white matter intensity values below 110, should I redo intensity normalization with control points on them as well? Thanks! Kelli
Hi, I'm trying to reorient some analyze files using mri_convert. The files are in LAS format and I'd like to get them in LPI format. i run the command below, but get the message: mri_convert: unknown flag "--in-orientation"
mri_convert -it analyze 1000001_lh_bound_gs -ot analyze ./1000001_lh_bound_gs_r.img --in-orientation LAS --out-orientation LPI
Any help is much appreciated! Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Never mind, I noticed that higher up in the usage it shows the command with an underscore (e.g., --in_orientation). Just to note, the final para about orientation in the usage uses a dash, ie., --in-orientation.This command does not work. Cheers, A
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Fornito, Alexander Sent: Tue 21/02/2006 9:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: mri_convert orientation
Hi, I'm trying to reorient some analyze files using mri_convert. The files are in LAS format and I'd like to get them in LPI format. i run the command below, but get the message: mri_convert: unknown flag "--in-orientation"
mri_convert -it analyze 1000001_lh_bound_gs -ot analyze ./1000001_lh_bound_gs_r.img --in-orientation LAS --out-orientation LPI
Any help is much appreciated! Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
The documentation is wrong, it should be --in_ and --out_ (note the underscore, not the dash).
But, read the rest of the documentation carefully and make sure this is going to do what you want it to do. It will NOT change the pixel data. It only changes the description of the geometry of the FOV and should only be used if this description is wrong.
doug
Fornito, Alexander wrote:
Hi, I'm trying to reorient some analyze files using mri_convert. The files are in LAS format and I'd like to get them in LPI format. i run the command below, but get the message: mri_convert: unknown flag "--in-orientation"
mri_convert -it analyze 1000001_lh_bound_gs -ot analyze ./1000001_lh_bound_gs_r.img --in-orientation LAS --out-orientation LPI
Any help is much appreciated! Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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Nick Schmansky